From ccec47c21c56226ffcbe6455a0788b100577ce1d Mon Sep 17 00:00:00 2001 From: Alex-Davydov <9384251+Alex-Davydov@users.noreply.github.com> Date: Thu, 27 Nov 2025 16:17:20 +0000 Subject: [PATCH] regression tests automated change --- regression/presets/analyze/10x-5gex-cdr3.yaml | 8 +-- .../presets/analyze/10x-5gex-full-length.yaml | 8 +-- regression/presets/analyze/10x-sc-5gex.yaml | 8 +-- .../presets/analyze/10x-sc-xcr-vdj-fast.yaml | 28 ++++---- .../analyze/10x-sc-xcr-vdj-gemx-v3.yaml | 28 ++++---- .../presets/analyze/10x-sc-xcr-vdj-rapid.yaml | 28 ++++---- .../presets/analyze/10x-sc-xcr-vdj.yaml | 28 ++++---- .../analyze/10x-vdj-bcr-full-length.yaml | 28 ++++---- regression/presets/analyze/10x-vdj-bcr.yaml | 28 ++++---- .../10x-vdj-tcr-alias-multi-barcode-test.yaml | 28 ++++---- .../analyze/10x-vdj-tcr-full-length.yaml | 28 ++++---- regression/presets/analyze/10x-vdj-tcr.yaml | 28 ++++---- .../analyze/abhelix-human-bcr-cdr3.yaml | 36 +++++----- .../abhelix-human-bcr-full-length.yaml | 36 +++++----- .../analyze/abhelix-human-rna-xcr.yaml | 36 +++++----- .../analyze/abhelix-human-tcr-cdr3.yaml | 36 +++++----- .../abhelix-human-tcr-full-length.yaml | 36 +++++----- .../analyze/ampliseq-tcrb-plus-cdr3.yaml | 36 +++++----- .../ampliseq-tcrb-plus-full-length.yaml | 36 +++++----- .../analyze/ampliseq-tcrb-sr-cdr3.yaml | 36 +++++----- .../bd-human-sc-xcr-rhapsody-cdr3.yaml | 72 +++++++++---------- .../bd-mouse-sc-xcr-rhapsody-cdr3.yaml | 72 +++++++++---------- .../bd-rhapsody-human-bcr-full-length.yaml | 28 ++++---- .../analyze/bd-rhapsody-human-bcr-v1.yaml | 72 +++++++++---------- .../analyze/bd-rhapsody-human-bcr-v2.yaml | 72 +++++++++---------- .../bd-rhapsody-human-tcr-full-length.yaml | 28 ++++---- .../analyze/bd-rhapsody-human-tcr-v1.yaml | 72 +++++++++---------- .../analyze/bd-rhapsody-human-tcr-v2.yaml | 72 +++++++++---------- .../bd-rhapsody-mouse-bcr-full-length.yaml | 28 ++++---- .../analyze/bd-rhapsody-mouse-bcr-v1.yaml | 72 +++++++++---------- .../analyze/bd-rhapsody-mouse-bcr-v2.yaml | 72 +++++++++---------- .../bd-rhapsody-mouse-tcr-full-length.yaml | 28 ++++---- .../analyze/bd-rhapsody-mouse-tcr-v1.yaml | 72 +++++++++---------- .../analyze/bd-rhapsody-mouse-tcr-v2.yaml | 72 +++++++++---------- ...rhapsody-full-length-enhanced-bead-v2.yaml | 28 ++++---- .../bd-sc-xcr-rhapsody-full-length.yaml | 28 ++++---- .../analyze/biomed2-human-bcr-cdr3.yaml | 36 +++++----- .../biomed2-human-bcr-full-length.yaml | 36 +++++----- .../analyze/biomed2-human-rna-igh.yaml | 36 +++++----- .../analyze/biomed2-human-rna-igkl.yaml | 32 ++++----- .../analyze/biomed2-human-rna-trbdg.yaml | 32 ++++----- .../analyze/bruker-sc-xcr-vdj-beacon.yaml | 36 +++++----- ...-human-dna-xcr-mivbc-drivermap-air-v2.yaml | 36 +++++----- ...lecta-human-dna-xcr-umi-drivermap-air.yaml | 68 +++++++++--------- ...cr-full-length-mivbc-drivermap-air-v2.yaml | 36 +++++----- ...rna-xcr-full-length-umi-drivermap-air.yaml | 68 +++++++++--------- ...-human-rna-xcr-mivbc-drivermap-air-v2.yaml | 36 +++++----- ...r-umi-drivermap-air-bcr-spikein-1-1-1.yaml | 68 +++++++++--------- ...-umi-drivermap-air-bcr-spikein-16-4-1.yaml | 68 +++++++++--------- ...r-umi-drivermap-air-tcr-spikein-1-1-1.yaml | 68 +++++++++--------- ...-umi-drivermap-air-tcr-spikein-16-4-1.yaml | 68 +++++++++--------- ...lecta-human-rna-xcr-umi-drivermap-air.yaml | 68 +++++++++--------- ...-mouse-rna-xcr-mivbc-drivermap-air-v2.yaml | 36 +++++----- ...lecta-mouse-rna-xcr-umi-drivermap-air.yaml | 68 +++++++++--------- regression/presets/analyze/exome-seq.yaml | 4 +- .../presets/analyze/flairr-seq-bcr.yaml | 64 ++++++++--------- .../analyze/generic-amplicon-with-umi.yaml | 64 ++++++++--------- .../presets/analyze/generic-amplicon.yaml | 32 ++++----- .../analyze/generic-bcr-amplicon-umi.yaml | 64 ++++++++--------- .../presets/analyze/generic-bcr-amplicon.yaml | 32 ++++----- ...eric-ht-single-cell-amplicon-with-umi.yaml | 72 +++++++++---------- .../generic-ht-single-cell-amplicon.yaml | 36 +++++----- ...ic-ht-single-cell-fragmented-with-umi.yaml | 28 ++++---- .../generic-ht-single-cell-fragmented.yaml | 28 ++++---- ...eric-lt-single-cell-amplicon-with-umi.yaml | 68 +++++++++--------- .../generic-lt-single-cell-amplicon.yaml | 36 +++++----- .../generic-lt-single-cell-fragmented.yaml | 16 ++--- .../presets/analyze/generic-ont-with-umi.yaml | 4 +- regression/presets/analyze/generic-ont.yaml | 4 +- .../analyze/generic-pacbio-with-umi.yaml | 4 +- .../presets/analyze/generic-pacbio.yaml | 4 +- .../generic-single-cell-gex-with-umi.yaml | 8 +-- .../analyze/generic-single-cell-gex.yaml | 8 +-- ...ric-tcr-amplicon-separate-samples-umi.yaml | 64 ++++++++--------- .../analyze/generic-tcr-amplicon-umi.yaml | 64 ++++++++--------- .../presets/analyze/generic-tcr-amplicon.yaml | 32 ++++----- .../presets/analyze/han-et-al-2014.yaml | 32 ++++----- .../analyze/idt-human-rna-bcr-umi-archer.yaml | 64 ++++++++--------- .../analyze/idt-human-rna-tcr-umi-archer.yaml | 64 ++++++++--------- .../illumina-human-dna-trb-ampliseq-sr.yaml | 36 +++++----- .../illumina-human-rna-trb-ampliseq-plus.yaml | 36 +++++----- .../illumina-human-rna-trb-ampliseq-sr.yaml | 36 +++++----- ...oscribe-human-dna-igh-fr1-lymphotrack.yaml | 32 ++++----- ...cribe-human-dna-igh-fr123-lymphotrack.yaml | 32 ++++----- ...oscribe-human-dna-igh-fr2-lymphotrack.yaml | 32 ++++----- ...oscribe-human-dna-igh-fr3-lymphotrack.yaml | 32 ++++----- ...ibe-human-dna-ighv-leader-lymphotrack.yaml | 32 ++++----- ...nvivoscribe-human-dna-igk-lymphotrack.yaml | 32 ++++----- ...nvivoscribe-human-dna-trb-lymphotrack.yaml | 32 ++++----- ...nvivoscribe-human-dna-trg-lymphotrack.yaml | 32 ++++----- .../analyze/irepertoire-human-dna-igh-lr.yaml | 32 ++++----- .../analyze/irepertoire-human-dna-igh-sr.yaml | 32 ++++----- .../analyze/irepertoire-human-dna-trb-lr.yaml | 32 ++++----- .../analyze/irepertoire-human-dna-trb-sr.yaml | 32 ++++----- .../irepertoire-human-dna-xcr-repseq-lr.yaml | 32 ++++----- .../irepertoire-human-dna-xcr-repseq-sr.yaml | 32 ++++----- .../analyze/irepertoire-human-rna-bcr-lr.yaml | 36 +++++----- .../analyze/irepertoire-human-rna-bcr-sr.yaml | 36 +++++----- .../analyze/irepertoire-human-rna-tcr-lr.yaml | 36 +++++----- .../analyze/irepertoire-human-rna-tcr-sr.yaml | 36 +++++----- .../irepertoire-human-rna-xcr-repseq-lr.yaml | 36 +++++----- ...oire-human-rna-xcr-repseq-plus-umi-pe.yaml | 64 ++++++++--------- ...oire-human-rna-xcr-repseq-plus-umi-se.yaml | 64 ++++++++--------- ...irepertoire-human-rna-xcr-repseq-plus.yaml | 36 +++++----- .../irepertoire-human-rna-xcr-repseq-sr.yaml | 36 +++++----- .../analyze/irepertoire-mouse-rna-bcr-lr.yaml | 36 +++++----- .../analyze/irepertoire-mouse-rna-bcr-sr.yaml | 36 +++++----- .../analyze/irepertoire-mouse-rna-tcr-lr.yaml | 36 +++++----- .../analyze/irepertoire-mouse-rna-tcr-sr.yaml | 36 +++++----- .../irepertoire-mouse-rna-xcr-repseq-lr.yaml | 36 +++++----- ...oire-mouse-rna-xcr-repseq-plus-umi-pe.yaml | 64 ++++++++--------- ...irepertoire-mouse-rna-xcr-repseq-plus.yaml | 36 +++++----- .../irepertoire-mouse-rna-xcr-repseq-sr.yaml | 36 +++++----- .../presets/analyze/mikelov-et-al-2021.yaml | 64 ++++++++--------- .../milab-human-bcr-multiplex-cdr3.yaml | 68 +++++++++--------- ...milab-human-bcr-multiplex-full-length.yaml | 68 +++++++++--------- .../milab-human-dna-tcr-multiplex.yaml | 36 +++++----- .../milab-human-dna-xcr-7genes-multiplex.yaml | 36 +++++----- .../milab-human-rna-ig-umi-multiplex.yaml | 68 +++++++++--------- .../milab-human-rna-tcr-umi-multiplex.yaml | 68 +++++++++--------- .../analyze/milab-human-rna-tcr-umi-race.yaml | 68 +++++++++--------- .../milab-human-tcr-dna-multiplex-cdr3.yaml | 36 +++++----- .../milab-human-tcr-rna-multiplex-cdr3.yaml | 68 +++++++++--------- .../milab-human-tcr-rna-race-cdr3.yaml | 68 +++++++++--------- .../milab-human-tcr-rna-race-full-length.yaml | 68 +++++++++--------- .../analyze/milab-mouse-rna-tcr-umi-race.yaml | 68 +++++++++--------- .../milab-mouse-tcr-rna-race-cdr3.yaml | 68 +++++++++--------- .../milab-mouse-tcr-rna-race-full-length.yaml | 68 +++++++++--------- .../neb-human-rna-xcr-umi-nebnext.yaml | 68 +++++++++--------- .../neb-mouse-rna-xcr-umi-nebnext.yaml | 68 +++++++++--------- .../analyze/nebnext-human-bcr-cdr3.yaml | 68 +++++++++--------- .../nebnext-human-bcr-full-length.yaml | 68 +++++++++--------- .../analyze/nebnext-human-tcr-bcr-cdr3.yaml | 68 +++++++++--------- .../nebnext-human-tcr-bcr-full-length.yaml | 68 +++++++++--------- .../analyze/nebnext-human-tcr-cdr3.yaml | 68 +++++++++--------- .../nebnext-human-tcr-full-length.yaml | 68 +++++++++--------- .../analyze/nebnext-mouse-bcr-cdr3.yaml | 68 +++++++++--------- .../nebnext-mouse-bcr-full-length.yaml | 68 +++++++++--------- .../analyze/nebnext-mouse-tcr-bcr-cdr3.yaml | 68 +++++++++--------- .../nebnext-mouse-tcr-bcr-full-length.yaml | 68 +++++++++--------- .../analyze/nebnext-mouse-tcr-cdr3.yaml | 68 +++++++++--------- .../nebnext-mouse-tcr-full-length.yaml | 68 +++++++++--------- .../oncomine-human-bcr-ihg-lr-cdr3.yaml | 32 ++++----- ...oncomine-human-bcr-ihg-lr-full-length.yaml | 32 ++++----- ...oncomine-human-bcr-pan-clonality-cdr3.yaml | 32 ++++----- .../analyze/oncomine-human-igh-fr1-j.yaml | 32 ++++----- .../analyze/oncomine-human-igh-fr2-j.yaml | 32 ++++----- .../analyze/oncomine-human-igh-fr3-j.yaml | 32 ++++----- .../analyze/oncomine-human-igh-leader-j.yaml | 32 ++++----- ...oncomine-human-tcr-pan-clonality-cdr3.yaml | 32 ++++----- .../analyze/oncomine-human-tcrb-lr-cdr3.yaml | 32 ++++----- .../oncomine-human-tcrb-lr-full-length.yaml | 32 ++++----- .../analyze/oncomine-human-tcrb-sr-cdr3.yaml | 32 ++++----- .../analyze/ont-rna-seq-vdj-full-length.yaml | 4 +- regression/presets/analyze/ont-rna-seq.yaml | 4 +- .../presets/analyze/parse-bio-vdj-3gex.yaml | 8 +-- .../parsebio-sc-3gex-evercode-wt-mega.yaml | 8 +-- .../parsebio-sc-3gex-evercode-wt-mini.yaml | 8 +-- .../analyze/parsebio-sc-3gex-evercode-wt.yaml | 8 +-- .../analyze/parsebio-sc-bcr-evercode.yaml | 28 ++++---- .../qiagen-human-rna-tcr-umi-qiaseq.yaml | 68 +++++++++--------- ...gen-human-rna-tcr-umi-targeted-qiaseq.yaml | 68 +++++++++--------- .../qiagen-mouse-rna-tcr-umi-qiaseq.yaml | 68 +++++++++--------- ...gen-mouse-rna-tcr-umi-targeted-qiaseq.yaml | 68 +++++++++--------- .../analyze/qiaseq-human-tcr-cdr3.yaml | 68 +++++++++--------- .../analyze/qiaseq-human-tcr-full-length.yaml | 68 +++++++++--------- .../analyze/qiaseq-mouse-tcr-cdr3.yaml | 68 +++++++++--------- .../analyze/qiaseq-mouse-tcr-full-length.yaml | 68 +++++++++--------- regression/presets/analyze/rna-seq.yaml | 4 +- regression/presets/analyze/seq-well-vdj.yaml | 72 +++++++++---------- .../presets/analyze/seqwell-vdj-cdr3.yaml | 72 +++++++++---------- .../analyze/singleron-2.0.1-vdj-cdr3.yaml | 72 +++++++++---------- .../singleron-human-sc-xcr-gexscope-vdj.yaml | 72 +++++++++---------- .../presets/analyze/smart-seq2-vdj.yaml | 8 +-- .../analyze/smartseq2-vdj-full-length.yaml | 8 +-- .../presets/analyze/split-seq-3gex.yaml | 8 +-- .../presets/analyze/split-seq-vdj-3gex.yaml | 8 +-- .../analyze/takara-human-bcr-cdr3.yaml | 68 +++++++++--------- .../analyze/takara-human-bcr-full-length.yaml | 68 +++++++++--------- .../takara-human-rna-bcr-umi-smarter.yaml | 68 +++++++++--------- .../takara-human-rna-bcr-umi-smartseq.yaml | 68 +++++++++--------- .../analyze/takara-human-rna-tcr-smarter.yaml | 36 +++++----- .../takara-human-rna-tcr-umi-smarter-v2.yaml | 68 +++++++++--------- .../takara-human-rna-tcr-umi-smartseq.yaml | 68 +++++++++--------- .../analyze/takara-human-tcr-V1-cdr3.yaml | 36 +++++----- .../takara-human-tcr-V1-full-length.yaml | 36 +++++----- .../analyze/takara-human-tcr-V2-cdr3.yaml | 68 +++++++++--------- .../takara-human-tcr-V2-full-length.yaml | 68 +++++++++--------- .../analyze/takara-mouse-bcr-cdr3.yaml | 36 +++++----- .../analyze/takara-mouse-bcr-full-length.yaml | 36 +++++----- .../analyze/takara-mouse-rna-bcr-smarter.yaml | 36 +++++----- .../takara-mouse-rna-bcr-umi-smarseq.yaml | 68 +++++++++--------- .../analyze/takara-mouse-rna-tcr-smarter.yaml | 36 +++++----- .../takara-mouse-rna-tcr-umi-smarseq.yaml | 68 +++++++++--------- .../analyze/takara-mouse-tcr-cdr3.yaml | 36 +++++----- .../analyze/takara-mouse-tcr-full-length.yaml | 36 +++++----- .../takara-sc-human-rna-tcr-smarter.yaml | 36 +++++----- .../presets/analyze/test-gf-intersection.yaml | 64 ++++++++--------- .../test-mikelov-et-al-2021-with-contigs.yaml | 64 ++++++++--------- ...st-mikelov-et-al-2021-without-contigs.yaml | 64 ++++++++--------- .../presets/analyze/test-tag-from-header.yaml | 32 ++++----- ...-human-dna-bcr-oncomine-pan-clonality.yaml | 32 ++++----- ...mofisher-human-dna-igh-oncomine-fr1-j.yaml | 32 ++++----- ...mofisher-human-dna-igh-oncomine-fr2-j.yaml | 32 ++++----- ...mofisher-human-dna-igh-oncomine-fr3-j.yaml | 32 ++++----- ...hermofisher-human-dna-igh-oncomine-sr.yaml | 32 ++++----- ...her-human-dna-igh-oncomine-v-leader-j.yaml | 32 ++++----- ...-human-dna-tcr-oncomine-pan-clonality.yaml | 32 ++++----- ...hermofisher-human-dna-trb-oncomine-sr.yaml | 32 ++++----- ...hermofisher-human-rna-igh-oncomine-lr.yaml | 32 ++++----- ...hermofisher-human-rna-igh-oncomine-sr.yaml | 32 ++++----- ...hermofisher-human-rna-trb-oncomine-lr.yaml | 32 ++++----- ...hermofisher-human-rna-trb-oncomine-sr.yaml | 32 ++++----- ...hermofisher-mouse-dna-igh-ampliseq-sr.yaml | 32 ++++----- ...hermofisher-mouse-dna-tcb-ampliseq-sr.yaml | 32 ++++----- ...hermofisher-mouse-rna-igh-ampliseq-sr.yaml | 32 ++++----- ...hermofisher-mouse-rna-tcb-ampliseq-sr.yaml | 32 ++++----- .../analyze/vergani-et-al-2017-cdr3.yaml | 64 ++++++++--------- .../vergani-et-al-2017-full-length.yaml | 64 ++++++++--------- 219 files changed, 4780 insertions(+), 4780 deletions(-) diff --git a/regression/presets/analyze/10x-5gex-cdr3.yaml b/regression/presets/analyze/10x-5gex-cdr3.yaml index 18c4534e7..48040081b 100644 --- a/regression/presets/analyze/10x-5gex-cdr3.yaml +++ b/regression/presets/analyze/10x-5gex-cdr3.yaml @@ -446,10 +446,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-5gex-full-length.yaml b/regression/presets/analyze/10x-5gex-full-length.yaml index 644ce689d..69096fecf 100644 --- a/regression/presets/analyze/10x-5gex-full-length.yaml +++ b/regression/presets/analyze/10x-5gex-full-length.yaml @@ -451,10 +451,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-sc-5gex.yaml b/regression/presets/analyze/10x-sc-5gex.yaml index 18c4534e7..48040081b 100644 --- a/regression/presets/analyze/10x-sc-5gex.yaml +++ b/regression/presets/analyze/10x-sc-5gex.yaml @@ -446,10 +446,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-sc-xcr-vdj-fast.yaml b/regression/presets/analyze/10x-sc-xcr-vdj-fast.yaml index 901f2d245..454a78364 100644 --- a/regression/presets/analyze/10x-sc-xcr-vdj-fast.yaml +++ b/regression/presets/analyze/10x-sc-xcr-vdj-fast.yaml @@ -729,31 +729,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-sc-xcr-vdj-gemx-v3.yaml b/regression/presets/analyze/10x-sc-xcr-vdj-gemx-v3.yaml index b1f01da72..3eeffd810 100644 --- a/regression/presets/analyze/10x-sc-xcr-vdj-gemx-v3.yaml +++ b/regression/presets/analyze/10x-sc-xcr-vdj-gemx-v3.yaml @@ -726,31 +726,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-sc-xcr-vdj-rapid.yaml b/regression/presets/analyze/10x-sc-xcr-vdj-rapid.yaml index 753b509f3..bff8785cf 100644 --- a/regression/presets/analyze/10x-sc-xcr-vdj-rapid.yaml +++ b/regression/presets/analyze/10x-sc-xcr-vdj-rapid.yaml @@ -585,31 +585,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-sc-xcr-vdj.yaml b/regression/presets/analyze/10x-sc-xcr-vdj.yaml index ea771dc86..aac81ff4c 100644 --- a/regression/presets/analyze/10x-sc-xcr-vdj.yaml +++ b/regression/presets/analyze/10x-sc-xcr-vdj.yaml @@ -726,31 +726,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml index ea771dc86..aac81ff4c 100644 --- a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml @@ -726,31 +726,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml index ea771dc86..aac81ff4c 100644 --- a/regression/presets/analyze/10x-vdj-bcr.yaml +++ b/regression/presets/analyze/10x-vdj-bcr.yaml @@ -726,31 +726,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml b/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml index 0b3b7ef06..230e9684b 100644 --- a/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml @@ -756,31 +756,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml index ea771dc86..aac81ff4c 100644 --- a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml +++ b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml @@ -726,31 +726,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/10x-vdj-tcr.yaml b/regression/presets/analyze/10x-vdj-tcr.yaml index ea771dc86..aac81ff4c 100644 --- a/regression/presets/analyze/10x-vdj-tcr.yaml +++ b/regression/presets/analyze/10x-vdj-tcr.yaml @@ -726,31 +726,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml index e80f525d7..6187980ce 100644 --- a/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/abhelix-human-bcr-full-length.yaml b/regression/presets/analyze/abhelix-human-bcr-full-length.yaml index 6a0dfb450..792b516f1 100644 --- a/regression/presets/analyze/abhelix-human-bcr-full-length.yaml +++ b/regression/presets/analyze/abhelix-human-bcr-full-length.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/abhelix-human-rna-xcr.yaml b/regression/presets/analyze/abhelix-human-rna-xcr.yaml index 6a0dfb450..792b516f1 100644 --- a/regression/presets/analyze/abhelix-human-rna-xcr.yaml +++ b/regression/presets/analyze/abhelix-human-rna-xcr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml index e80f525d7..6187980ce 100644 --- a/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml +++ b/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/abhelix-human-tcr-full-length.yaml b/regression/presets/analyze/abhelix-human-tcr-full-length.yaml index 6a0dfb450..792b516f1 100644 --- a/regression/presets/analyze/abhelix-human-tcr-full-length.yaml +++ b/regression/presets/analyze/abhelix-human-tcr-full-length.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml index b49b1e9a2..bdc1cc36e 100644 --- a/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml index 3ecf87a1e..c2ae88742 100644 --- a/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml index 3ecf87a1e..c2ae88742 100644 --- a/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml +++ b/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml b/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml index 0a61a5051..0d112f9cb 100644 --- a/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml +++ b/regression/presets/analyze/bd-human-sc-xcr-rhapsody-cdr3.yaml @@ -1190,77 +1190,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml b/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml index 7ef0e9db4..b18ccdcaa 100644 --- a/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml +++ b/regression/presets/analyze/bd-mouse-sc-xcr-rhapsody-cdr3.yaml @@ -1195,77 +1195,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml index 98fb2d685..55ed174a9 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml @@ -1188,31 +1188,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml index 0a61a5051..0d112f9cb 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml @@ -1190,77 +1190,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml index 0a61a5051..0d112f9cb 100644 --- a/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml @@ -1190,77 +1190,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml index 98fb2d685..55ed174a9 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml @@ -1188,31 +1188,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml index 0a61a5051..0d112f9cb 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml @@ -1190,77 +1190,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml index 0a61a5051..0d112f9cb 100644 --- a/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml @@ -1190,77 +1190,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml index 98fb2d685..55ed174a9 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml @@ -1188,31 +1188,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml index 7ef0e9db4..b18ccdcaa 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml @@ -1195,77 +1195,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml index 7ef0e9db4..b18ccdcaa 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml @@ -1195,77 +1195,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml index 98fb2d685..55ed174a9 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml @@ -1188,31 +1188,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml index 7ef0e9db4..b18ccdcaa 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml @@ -1195,77 +1195,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml index 7ef0e9db4..b18ccdcaa 100644 --- a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml +++ b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml @@ -1195,77 +1195,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2.yaml b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2.yaml index b9bb7d5bf..d54879884 100644 --- a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2.yaml +++ b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2.yaml @@ -2916,31 +2916,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml index 98fb2d685..55ed174a9 100644 --- a/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml +++ b/regression/presets/analyze/bd-sc-xcr-rhapsody-full-length.yaml @@ -1188,31 +1188,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml b/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml index ba95de3df..eb577ae2f 100644 --- a/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/biomed2-human-bcr-full-length.yaml b/regression/presets/analyze/biomed2-human-bcr-full-length.yaml index 62d3c97d3..4445d401c 100644 --- a/regression/presets/analyze/biomed2-human-bcr-full-length.yaml +++ b/regression/presets/analyze/biomed2-human-bcr-full-length.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/biomed2-human-rna-igh.yaml b/regression/presets/analyze/biomed2-human-rna-igh.yaml index 62d3c97d3..4445d401c 100644 --- a/regression/presets/analyze/biomed2-human-rna-igh.yaml +++ b/regression/presets/analyze/biomed2-human-rna-igh.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/biomed2-human-rna-igkl.yaml b/regression/presets/analyze/biomed2-human-rna-igkl.yaml index 4a0e96d5f..dbd90c9bb 100644 --- a/regression/presets/analyze/biomed2-human-rna-igkl.yaml +++ b/regression/presets/analyze/biomed2-human-rna-igkl.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/biomed2-human-rna-trbdg.yaml b/regression/presets/analyze/biomed2-human-rna-trbdg.yaml index 4a0e96d5f..dbd90c9bb 100644 --- a/regression/presets/analyze/biomed2-human-rna-trbdg.yaml +++ b/regression/presets/analyze/biomed2-human-rna-trbdg.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml b/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml index 19177819a..01d531d16 100644 --- a/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml +++ b/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml @@ -577,38 +577,38 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/cellecta-human-dna-xcr-mivbc-drivermap-air-v2.yaml b/regression/presets/analyze/cellecta-human-dna-xcr-mivbc-drivermap-air-v2.yaml index e9a5745a6..d6c3949b8 100644 --- a/regression/presets/analyze/cellecta-human-dna-xcr-mivbc-drivermap-air-v2.yaml +++ b/regression/presets/analyze/cellecta-human-dna-xcr-mivbc-drivermap-air-v2.yaml @@ -334,38 +334,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml index 1f11d8ee8..c1bc7b4fc 100644 --- a/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml +++ b/regression/presets/analyze/cellecta-human-dna-xcr-umi-drivermap-air.yaml @@ -382,72 +382,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-full-length-mivbc-drivermap-air-v2.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-full-length-mivbc-drivermap-air-v2.yaml index dbb75d1cc..3b42e044d 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-full-length-mivbc-drivermap-air-v2.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-full-length-mivbc-drivermap-air-v2.yaml @@ -362,38 +362,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml index 1c4b5e05b..d8050e5ea 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-full-length-umi-drivermap-air.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-mivbc-drivermap-air-v2.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-mivbc-drivermap-air-v2.yaml index bcb5076f7..96305698f 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-mivbc-drivermap-air-v2.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-mivbc-drivermap-air-v2.yaml @@ -362,38 +362,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-1-1-1.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-1-1-1.yaml index 895139913..b2d96b80f 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-1-1-1.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-1-1-1.yaml @@ -410,74 +410,74 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads - type: SpikeInControls alphabet: Nucleotide diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-16-4-1.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-16-4-1.yaml index ea249491c..149ffea25 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-16-4-1.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-bcr-spikein-16-4-1.yaml @@ -410,74 +410,74 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads - type: SpikeInControls alphabet: Nucleotide diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-1-1-1.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-1-1-1.yaml index 5b2c9255c..7db37966e 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-1-1-1.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-1-1-1.yaml @@ -410,74 +410,74 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads - type: SpikeInControls alphabet: Nucleotide diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-16-4-1.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-16-4-1.yaml index a0e917942..f8a08b297 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-16-4-1.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air-tcr-spikein-16-4-1.yaml @@ -410,74 +410,74 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads - type: SpikeInControls alphabet: Nucleotide diff --git a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air.yaml index f19613ee6..70372f1a9 100644 --- a/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air.yaml +++ b/regression/presets/analyze/cellecta-human-rna-xcr-umi-drivermap-air.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/cellecta-mouse-rna-xcr-mivbc-drivermap-air-v2.yaml b/regression/presets/analyze/cellecta-mouse-rna-xcr-mivbc-drivermap-air-v2.yaml index 14c2a8077..976a44b44 100644 --- a/regression/presets/analyze/cellecta-mouse-rna-xcr-mivbc-drivermap-air-v2.yaml +++ b/regression/presets/analyze/cellecta-mouse-rna-xcr-mivbc-drivermap-air-v2.yaml @@ -362,38 +362,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/cellecta-mouse-rna-xcr-umi-drivermap-air.yaml b/regression/presets/analyze/cellecta-mouse-rna-xcr-umi-drivermap-air.yaml index e39308909..7bd328dcb 100644 --- a/regression/presets/analyze/cellecta-mouse-rna-xcr-umi-drivermap-air.yaml +++ b/regression/presets/analyze/cellecta-mouse-rna-xcr-umi-drivermap-air.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/exome-seq.yaml b/regression/presets/analyze/exome-seq.yaml index 4b4f7d8b3..4bc9f7948 100644 --- a/regression/presets/analyze/exome-seq.yaml +++ b/regression/presets/analyze/exome-seq.yaml @@ -324,6 +324,6 @@ exportClones: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality diff --git a/regression/presets/analyze/flairr-seq-bcr.yaml b/regression/presets/analyze/flairr-seq-bcr.yaml index 3df4fa564..d03545023 100644 --- a/regression/presets/analyze/flairr-seq-bcr.yaml +++ b/regression/presets/analyze/flairr-seq-bcr.yaml @@ -411,68 +411,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/generic-amplicon-with-umi.yaml b/regression/presets/analyze/generic-amplicon-with-umi.yaml index cc70cc81e..58dc9d369 100644 --- a/regression/presets/analyze/generic-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-amplicon-with-umi.yaml @@ -415,68 +415,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/generic-amplicon.yaml b/regression/presets/analyze/generic-amplicon.yaml index 9cba6784b..512ec0ac3 100644 --- a/regression/presets/analyze/generic-amplicon.yaml +++ b/regression/presets/analyze/generic-amplicon.yaml @@ -335,34 +335,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/generic-bcr-amplicon-umi.yaml b/regression/presets/analyze/generic-bcr-amplicon-umi.yaml index cc70cc81e..58dc9d369 100644 --- a/regression/presets/analyze/generic-bcr-amplicon-umi.yaml +++ b/regression/presets/analyze/generic-bcr-amplicon-umi.yaml @@ -415,68 +415,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/generic-bcr-amplicon.yaml b/regression/presets/analyze/generic-bcr-amplicon.yaml index 9cba6784b..512ec0ac3 100644 --- a/regression/presets/analyze/generic-bcr-amplicon.yaml +++ b/regression/presets/analyze/generic-bcr-amplicon.yaml @@ -335,34 +335,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml b/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml index 3acd74ae2..300b3b5b5 100644 --- a/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-amplicon-with-umi.yaml @@ -549,77 +549,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml b/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml index b16437d47..a893cc392 100644 --- a/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-amplicon.yaml @@ -483,38 +483,38 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml b/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml index 86a79f9d5..ba97df929 100644 --- a/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-fragmented-with-umi.yaml @@ -554,31 +554,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml b/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml index 042e641a2..2a91098f4 100644 --- a/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml +++ b/regression/presets/analyze/generic-ht-single-cell-fragmented.yaml @@ -488,31 +488,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml b/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml index a8ff7307e..768dec0e6 100644 --- a/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-amplicon-with-umi.yaml @@ -516,72 +516,72 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml b/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml index 8cde65678..fc701c67b 100644 --- a/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-amplicon.yaml @@ -454,38 +454,38 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml b/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml index cc766171b..f7b9184ef 100644 --- a/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml +++ b/regression/presets/analyze/generic-lt-single-cell-fragmented.yaml @@ -459,18 +459,18 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/generic-ont-with-umi.yaml b/regression/presets/analyze/generic-ont-with-umi.yaml index 7eb762576..7591ab807 100644 --- a/regression/presets/analyze/generic-ont-with-umi.yaml +++ b/regression/presets/analyze/generic-ont-with-umi.yaml @@ -410,6 +410,6 @@ exportClones: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: Alignments dropped due to low sequence quality diff --git a/regression/presets/analyze/generic-ont.yaml b/regression/presets/analyze/generic-ont.yaml index 93f2a393b..f657243e1 100644 --- a/regression/presets/analyze/generic-ont.yaml +++ b/regression/presets/analyze/generic-ont.yaml @@ -333,6 +333,6 @@ exportClones: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: Alignments dropped due to low sequence quality diff --git a/regression/presets/analyze/generic-pacbio-with-umi.yaml b/regression/presets/analyze/generic-pacbio-with-umi.yaml index dca24b802..26d0c693b 100644 --- a/regression/presets/analyze/generic-pacbio-with-umi.yaml +++ b/regression/presets/analyze/generic-pacbio-with-umi.yaml @@ -409,6 +409,6 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads diff --git a/regression/presets/analyze/generic-pacbio.yaml b/regression/presets/analyze/generic-pacbio.yaml index 16810347a..4c35c28f8 100644 --- a/regression/presets/analyze/generic-pacbio.yaml +++ b/regression/presets/analyze/generic-pacbio.yaml @@ -332,6 +332,6 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads diff --git a/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml b/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml index 72c5ed9b1..865e23624 100644 --- a/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml +++ b/regression/presets/analyze/generic-single-cell-gex-with-umi.yaml @@ -446,10 +446,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/generic-single-cell-gex.yaml b/regression/presets/analyze/generic-single-cell-gex.yaml index cbdd6bc4a..e2ea5f4db 100644 --- a/regression/presets/analyze/generic-single-cell-gex.yaml +++ b/regression/presets/analyze/generic-single-cell-gex.yaml @@ -431,10 +431,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml b/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml index cc70cc81e..58dc9d369 100644 --- a/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon-separate-samples-umi.yaml @@ -415,68 +415,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/generic-tcr-amplicon-umi.yaml b/regression/presets/analyze/generic-tcr-amplicon-umi.yaml index cc70cc81e..58dc9d369 100644 --- a/regression/presets/analyze/generic-tcr-amplicon-umi.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon-umi.yaml @@ -415,68 +415,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/generic-tcr-amplicon.yaml b/regression/presets/analyze/generic-tcr-amplicon.yaml index 9cba6784b..512ec0ac3 100644 --- a/regression/presets/analyze/generic-tcr-amplicon.yaml +++ b/regression/presets/analyze/generic-tcr-amplicon.yaml @@ -335,34 +335,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/han-et-al-2014.yaml b/regression/presets/analyze/han-et-al-2014.yaml index 60462099d..e974ffe1a 100644 --- a/regression/presets/analyze/han-et-al-2014.yaml +++ b/regression/presets/analyze/han-et-al-2014.yaml @@ -481,34 +481,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/idt-human-rna-bcr-umi-archer.yaml b/regression/presets/analyze/idt-human-rna-bcr-umi-archer.yaml index 3e95aab4b..4c149dfd9 100644 --- a/regression/presets/analyze/idt-human-rna-bcr-umi-archer.yaml +++ b/regression/presets/analyze/idt-human-rna-bcr-umi-archer.yaml @@ -413,68 +413,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/idt-human-rna-tcr-umi-archer.yaml b/regression/presets/analyze/idt-human-rna-tcr-umi-archer.yaml index cc2be64d8..c06d16669 100644 --- a/regression/presets/analyze/idt-human-rna-tcr-umi-archer.yaml +++ b/regression/presets/analyze/idt-human-rna-tcr-umi-archer.yaml @@ -410,68 +410,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/illumina-human-dna-trb-ampliseq-sr.yaml b/regression/presets/analyze/illumina-human-dna-trb-ampliseq-sr.yaml index 3c32bdc5c..d4ed66252 100644 --- a/regression/presets/analyze/illumina-human-dna-trb-ampliseq-sr.yaml +++ b/regression/presets/analyze/illumina-human-dna-trb-ampliseq-sr.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml index b49b1e9a2..bdc1cc36e 100644 --- a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml +++ b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-plus.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml index 3ecf87a1e..c2ae88742 100644 --- a/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml +++ b/regression/presets/analyze/illumina-human-rna-trb-ampliseq-sr.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/invivoscribe-human-dna-igh-fr1-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igh-fr1-lymphotrack.yaml index 6d1e0d9cd..629a541c0 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igh-fr1-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igh-fr1-lymphotrack.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/invivoscribe-human-dna-igh-fr123-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igh-fr123-lymphotrack.yaml index 6d1e0d9cd..629a541c0 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igh-fr123-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igh-fr123-lymphotrack.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/invivoscribe-human-dna-igh-fr2-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igh-fr2-lymphotrack.yaml index c0b3177ec..c5006304b 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igh-fr2-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igh-fr2-lymphotrack.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/invivoscribe-human-dna-igh-fr3-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igh-fr3-lymphotrack.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igh-fr3-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igh-fr3-lymphotrack.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/invivoscribe-human-dna-ighv-leader-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-ighv-leader-lymphotrack.yaml index c409b4dbd..3f57dc8b0 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-ighv-leader-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-ighv-leader-lymphotrack.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/invivoscribe-human-dna-igk-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-igk-lymphotrack.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-igk-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-igk-lymphotrack.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/invivoscribe-human-dna-trb-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-trb-lymphotrack.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-trb-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-trb-lymphotrack.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/invivoscribe-human-dna-trg-lymphotrack.yaml b/regression/presets/analyze/invivoscribe-human-dna-trg-lymphotrack.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/invivoscribe-human-dna-trg-lymphotrack.yaml +++ b/regression/presets/analyze/invivoscribe-human-dna-trg-lymphotrack.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml index 617a4e3d7..1613120bd 100644 --- a/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-igh-lr.yaml @@ -303,36 +303,36 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter upper: 0.9 diff --git a/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml index 3c32bdc5c..ce50124b6 100644 --- a/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-igh-sr.yaml @@ -303,36 +303,36 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter upper: 0.9 diff --git a/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml index 617a4e3d7..1613120bd 100644 --- a/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-trb-lr.yaml @@ -303,36 +303,36 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter upper: 0.9 diff --git a/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml index 3c32bdc5c..ce50124b6 100644 --- a/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-trb-sr.yaml @@ -303,36 +303,36 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter upper: 0.9 diff --git a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml index 617a4e3d7..1613120bd 100644 --- a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-lr.yaml @@ -303,36 +303,36 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter upper: 0.9 diff --git a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml index 3c32bdc5c..ce50124b6 100644 --- a/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-dna-xcr-repseq-sr.yaml @@ -303,36 +303,36 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter upper: 0.9 diff --git a/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml index d7dec38e7..9db9b935f 100644 --- a/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-bcr-lr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml index bd694f1e1..e748baf42 100644 --- a/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-bcr-sr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml index d7dec38e7..9db9b935f 100644 --- a/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-tcr-lr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml index bd694f1e1..e748baf42 100644 --- a/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-tcr-sr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml index d7dec38e7..9db9b935f 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-lr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-pe.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-pe.yaml index 945d00bc6..8f4f5d84d 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-pe.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-pe.yaml @@ -410,70 +410,70 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter upper: 0.9 diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-se.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-se.yaml index 2fed6430c..afd7a823b 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-se.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus-umi-se.yaml @@ -410,70 +410,70 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter upper: 0.9 diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml index 0b85d4101..d293c6583 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-plus.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml index bd694f1e1..e748baf42 100644 --- a/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml +++ b/regression/presets/analyze/irepertoire-human-rna-xcr-repseq-sr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml index 2af86024f..9d50496d0 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-bcr-lr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml index 57b7a0e35..c591c072a 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-bcr-sr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml index 2af86024f..9d50496d0 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-tcr-lr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml index 57b7a0e35..c591c072a 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-tcr-sr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml index 2af86024f..9d50496d0 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-lr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus-umi-pe.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus-umi-pe.yaml index a955c6da0..7d2a6b5b4 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus-umi-pe.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus-umi-pe.yaml @@ -410,70 +410,70 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter upper: 0.9 diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml index 2af86024f..9d50496d0 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-plus.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml index 57b7a0e35..c591c072a 100644 --- a/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml +++ b/regression/presets/analyze/irepertoire-mouse-rna-xcr-repseq-sr.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/mikelov-et-al-2021.yaml b/regression/presets/analyze/mikelov-et-al-2021.yaml index b1acdb73e..41e73a69b 100644 --- a/regression/presets/analyze/mikelov-et-al-2021.yaml +++ b/regression/presets/analyze/mikelov-et-al-2021.yaml @@ -436,68 +436,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml b/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml index 803b2c347..231ee7fc6 100644 --- a/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml +++ b/regression/presets/analyze/milab-human-bcr-multiplex-cdr3.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml b/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml index 880fb6ea3..6e6e0afb8 100644 --- a/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml +++ b/regression/presets/analyze/milab-human-bcr-multiplex-full-length.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-dna-tcr-multiplex.yaml b/regression/presets/analyze/milab-human-dna-tcr-multiplex.yaml index ccdd29fbb..e6ac3956b 100644 --- a/regression/presets/analyze/milab-human-dna-tcr-multiplex.yaml +++ b/regression/presets/analyze/milab-human-dna-tcr-multiplex.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-dna-xcr-7genes-multiplex.yaml b/regression/presets/analyze/milab-human-dna-xcr-7genes-multiplex.yaml index ccdd29fbb..e6ac3956b 100644 --- a/regression/presets/analyze/milab-human-dna-xcr-7genes-multiplex.yaml +++ b/regression/presets/analyze/milab-human-dna-xcr-7genes-multiplex.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-rna-ig-umi-multiplex.yaml b/regression/presets/analyze/milab-human-rna-ig-umi-multiplex.yaml index 880fb6ea3..6e6e0afb8 100644 --- a/regression/presets/analyze/milab-human-rna-ig-umi-multiplex.yaml +++ b/regression/presets/analyze/milab-human-rna-ig-umi-multiplex.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-rna-tcr-umi-multiplex.yaml b/regression/presets/analyze/milab-human-rna-tcr-umi-multiplex.yaml index 02b4df273..e0d976852 100644 --- a/regression/presets/analyze/milab-human-rna-tcr-umi-multiplex.yaml +++ b/regression/presets/analyze/milab-human-rna-tcr-umi-multiplex.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-rna-tcr-umi-race.yaml b/regression/presets/analyze/milab-human-rna-tcr-umi-race.yaml index 8802f04bf..176fe9b4d 100644 --- a/regression/presets/analyze/milab-human-rna-tcr-umi-race.yaml +++ b/regression/presets/analyze/milab-human-rna-tcr-umi-race.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml b/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml index ccdd29fbb..e6ac3956b 100644 --- a/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml +++ b/regression/presets/analyze/milab-human-tcr-dna-multiplex-cdr3.yaml @@ -303,38 +303,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml b/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml index 02b4df273..e0d976852 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-multiplex-cdr3.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml b/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml index 8802f04bf..176fe9b4d 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-race-cdr3.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml b/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml index 8802f04bf..176fe9b4d 100644 --- a/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml +++ b/regression/presets/analyze/milab-human-tcr-rna-race-full-length.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-mouse-rna-tcr-umi-race.yaml b/regression/presets/analyze/milab-mouse-rna-tcr-umi-race.yaml index 39ce3cf34..0946bd9d4 100644 --- a/regression/presets/analyze/milab-mouse-rna-tcr-umi-race.yaml +++ b/regression/presets/analyze/milab-mouse-rna-tcr-umi-race.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml b/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml index 39ce3cf34..0946bd9d4 100644 --- a/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml +++ b/regression/presets/analyze/milab-mouse-tcr-rna-race-cdr3.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml b/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml index 39ce3cf34..0946bd9d4 100644 --- a/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml +++ b/regression/presets/analyze/milab-mouse-tcr-rna-race-full-length.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml b/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml index 6b298af83..738a7f4d0 100644 --- a/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml +++ b/regression/presets/analyze/neb-human-rna-xcr-umi-nebnext.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml b/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml index cc6a09568..41e26b217 100644 --- a/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml +++ b/regression/presets/analyze/neb-mouse-rna-xcr-umi-nebnext.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml index 3d80b9fa4..3c38663f7 100644 --- a/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-human-bcr-cdr3.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-human-bcr-full-length.yaml b/regression/presets/analyze/nebnext-human-bcr-full-length.yaml index 6b298af83..738a7f4d0 100644 --- a/regression/presets/analyze/nebnext-human-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-human-bcr-full-length.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml index 3d80b9fa4..3c38663f7 100644 --- a/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-bcr-cdr3.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml b/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml index 6b298af83..738a7f4d0 100644 --- a/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-bcr-full-length.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml b/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml index 3d80b9fa4..3c38663f7 100644 --- a/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-cdr3.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-human-tcr-full-length.yaml b/regression/presets/analyze/nebnext-human-tcr-full-length.yaml index 6b298af83..738a7f4d0 100644 --- a/regression/presets/analyze/nebnext-human-tcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-human-tcr-full-length.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml index eb58621cc..2d9df0562 100644 --- a/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-mouse-bcr-cdr3.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml index cc6a09568..41e26b217 100644 --- a/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-mouse-bcr-full-length.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml index eb58621cc..2d9df0562 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-bcr-cdr3.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml index cc6a09568..41e26b217 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-bcr-full-length.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml b/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml index eb58621cc..2d9df0562 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-cdr3.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml b/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml index cc6a09568..41e26b217 100644 --- a/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/nebnext-mouse-tcr-full-length.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.8 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml index 1f119d8b3..50bac34ce 100644 --- a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-cdr3.yaml @@ -334,34 +334,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml index 66b0aca3c..27a4231e5 100644 --- a/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-ihg-lr-full-length.yaml @@ -334,34 +334,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml b/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-bcr-pan-clonality-cdr3.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml index 6d1e0d9cd..629a541c0 100644 --- a/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-fr1-j.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml index c0b3177ec..c5006304b 100644 --- a/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-fr2-j.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml b/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-fr3-j.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-igh-leader-j.yaml b/regression/presets/analyze/oncomine-human-igh-leader-j.yaml index c409b4dbd..3f57dc8b0 100644 --- a/regression/presets/analyze/oncomine-human-igh-leader-j.yaml +++ b/regression/presets/analyze/oncomine-human-igh-leader-j.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-tcr-pan-clonality-cdr3.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml index 78d9fe2b7..69d1aa0f0 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-lr-cdr3.yaml @@ -331,34 +331,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml b/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml index 65cf00502..b6421793e 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-lr-full-length.yaml @@ -331,34 +331,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml b/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml index 4a0e96d5f..dbd90c9bb 100644 --- a/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml +++ b/regression/presets/analyze/oncomine-human-tcrb-sr-cdr3.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml b/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml index 93f2a393b..f657243e1 100644 --- a/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml +++ b/regression/presets/analyze/ont-rna-seq-vdj-full-length.yaml @@ -333,6 +333,6 @@ exportClones: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: Alignments dropped due to low sequence quality diff --git a/regression/presets/analyze/ont-rna-seq.yaml b/regression/presets/analyze/ont-rna-seq.yaml index 93f2a393b..f657243e1 100644 --- a/regression/presets/analyze/ont-rna-seq.yaml +++ b/regression/presets/analyze/ont-rna-seq.yaml @@ -333,6 +333,6 @@ exportClones: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: Alignments dropped due to low sequence quality diff --git a/regression/presets/analyze/parse-bio-vdj-3gex.yaml b/regression/presets/analyze/parse-bio-vdj-3gex.yaml index 918de5a2a..fc610c592 100644 --- a/regression/presets/analyze/parse-bio-vdj-3gex.yaml +++ b/regression/presets/analyze/parse-bio-vdj-3gex.yaml @@ -1254,10 +1254,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml index 918de5a2a..fc610c592 100644 --- a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml +++ b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mega.yaml @@ -1254,10 +1254,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml index fc3ade0f5..57d3af2c9 100644 --- a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml +++ b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt-mini.yaml @@ -918,10 +918,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml index 92343dcc2..fcef1837a 100644 --- a/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml +++ b/regression/presets/analyze/parsebio-sc-3gex-evercode-wt.yaml @@ -1062,10 +1062,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/parsebio-sc-bcr-evercode.yaml b/regression/presets/analyze/parsebio-sc-bcr-evercode.yaml index b380a4316..5e7c2aff9 100644 --- a/regression/presets/analyze/parsebio-sc-bcr-evercode.yaml +++ b/regression/presets/analyze/parsebio-sc-bcr-evercode.yaml @@ -1376,31 +1376,31 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.8 - middle: 0.6 + upper: 0.6 + middle: 0.4 label: Successfully aligned reads - type: UnassignedAlignments - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Unassigned alignments in clonotype assembly - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: ReadsDroppedInTagRefinement - upper: 0.3 - middle: 0.15 + upper: 0.5 + middle: 0.3 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagFiltering - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads dropped in tags filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml b/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml index 3ca8602ce..d2c3fa565 100644 --- a/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml +++ b/regression/presets/analyze/qiagen-human-rna-tcr-umi-qiaseq.yaml @@ -425,72 +425,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsLessBetter - upper: 0.1 - middle: 0.05 + upper: 0.2 + middle: 0.1 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/qiagen-human-rna-tcr-umi-targeted-qiaseq.yaml b/regression/presets/analyze/qiagen-human-rna-tcr-umi-targeted-qiaseq.yaml index 84c1e9c9b..98b7f74a7 100644 --- a/regression/presets/analyze/qiagen-human-rna-tcr-umi-targeted-qiaseq.yaml +++ b/regression/presets/analyze/qiagen-human-rna-tcr-umi-targeted-qiaseq.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsLessBetter - upper: 0.1 - middle: 0.05 + upper: 0.2 + middle: 0.1 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml b/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml index 441405706..9dcd4e0cc 100644 --- a/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml +++ b/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-qiaseq.yaml @@ -425,72 +425,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsLessBetter - upper: 0.1 - middle: 0.05 + upper: 0.2 + middle: 0.1 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-targeted-qiaseq.yaml b/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-targeted-qiaseq.yaml index b02088c5b..94da8733e 100644 --- a/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-targeted-qiaseq.yaml +++ b/regression/presets/analyze/qiagen-mouse-rna-tcr-umi-targeted-qiaseq.yaml @@ -410,72 +410,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsLessBetter - upper: 0.1 - middle: 0.05 + upper: 0.2 + middle: 0.1 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml b/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml index a134e7d3b..097416e16 100644 --- a/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml +++ b/regression/presets/analyze/qiaseq-human-tcr-cdr3.yaml @@ -425,72 +425,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsLessBetter - upper: 0.1 - middle: 0.05 + upper: 0.2 + middle: 0.1 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml b/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml index 3ca8602ce..d2c3fa565 100644 --- a/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml +++ b/regression/presets/analyze/qiaseq-human-tcr-full-length.yaml @@ -425,72 +425,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsLessBetter - upper: 0.1 - middle: 0.05 + upper: 0.2 + middle: 0.1 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml b/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml index 3d282d9dc..dcf5cff00 100644 --- a/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml +++ b/regression/presets/analyze/qiaseq-mouse-tcr-cdr3.yaml @@ -425,72 +425,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsLessBetter - upper: 0.1 - middle: 0.05 + upper: 0.2 + middle: 0.1 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml b/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml index 441405706..9dcd4e0cc 100644 --- a/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/qiaseq-mouse-tcr-full-length.yaml @@ -425,72 +425,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsLessBetter - upper: 0.1 - middle: 0.05 + upper: 0.2 + middle: 0.1 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/rna-seq.yaml b/regression/presets/analyze/rna-seq.yaml index b2bb14fb2..635677653 100644 --- a/regression/presets/analyze/rna-seq.yaml +++ b/regression/presets/analyze/rna-seq.yaml @@ -352,6 +352,6 @@ exportClones: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality diff --git a/regression/presets/analyze/seq-well-vdj.yaml b/regression/presets/analyze/seq-well-vdj.yaml index 7fc43ffb6..6b1a49b98 100644 --- a/regression/presets/analyze/seq-well-vdj.yaml +++ b/regression/presets/analyze/seq-well-vdj.yaml @@ -546,77 +546,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/seqwell-vdj-cdr3.yaml b/regression/presets/analyze/seqwell-vdj-cdr3.yaml index 7fc43ffb6..6b1a49b98 100644 --- a/regression/presets/analyze/seqwell-vdj-cdr3.yaml +++ b/regression/presets/analyze/seqwell-vdj-cdr3.yaml @@ -546,77 +546,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml b/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml index d2cd8a93c..0a72598e1 100644 --- a/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml +++ b/regression/presets/analyze/singleron-2.0.1-vdj-cdr3.yaml @@ -517,77 +517,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml b/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml index d2cd8a93c..0a72598e1 100644 --- a/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml +++ b/regression/presets/analyze/singleron-human-sc-xcr-gexscope-vdj.yaml @@ -517,77 +517,77 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: TagArtificialDiversityEliminated tag: CELL - upper: 0.8 - middle: 0.7 + upper: 0.9 + middle: 0.8 label: CELLs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/smart-seq2-vdj.yaml b/regression/presets/analyze/smart-seq2-vdj.yaml index e6831f7a4..8e698c2a3 100644 --- a/regression/presets/analyze/smart-seq2-vdj.yaml +++ b/regression/presets/analyze/smart-seq2-vdj.yaml @@ -431,10 +431,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/smartseq2-vdj-full-length.yaml b/regression/presets/analyze/smartseq2-vdj-full-length.yaml index e6831f7a4..8e698c2a3 100644 --- a/regression/presets/analyze/smartseq2-vdj-full-length.yaml +++ b/regression/presets/analyze/smartseq2-vdj-full-length.yaml @@ -431,10 +431,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/split-seq-3gex.yaml b/regression/presets/analyze/split-seq-3gex.yaml index 265e38d46..e71bbb3a7 100644 --- a/regression/presets/analyze/split-seq-3gex.yaml +++ b/regression/presets/analyze/split-seq-3gex.yaml @@ -1060,10 +1060,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/split-seq-vdj-3gex.yaml b/regression/presets/analyze/split-seq-vdj-3gex.yaml index 265e38d46..e71bbb3a7 100644 --- a/regression/presets/analyze/split-seq-vdj-3gex.yaml +++ b/regression/presets/analyze/split-seq-vdj-3gex.yaml @@ -1060,10 +1060,10 @@ exportCloneGroups: qc: checks: - type: AlignmentsDroppedLowQuality - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Alignments dropped due to low sequence quality - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/takara-human-bcr-cdr3.yaml b/regression/presets/analyze/takara-human-bcr-cdr3.yaml index cc506f037..9fe00aba5 100644 --- a/regression/presets/analyze/takara-human-bcr-cdr3.yaml +++ b/regression/presets/analyze/takara-human-bcr-cdr3.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-bcr-full-length.yaml b/regression/presets/analyze/takara-human-bcr-full-length.yaml index c077b159f..a8ef93457 100644 --- a/regression/presets/analyze/takara-human-bcr-full-length.yaml +++ b/regression/presets/analyze/takara-human-bcr-full-length.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml b/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml index c077b159f..a8ef93457 100644 --- a/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml +++ b/regression/presets/analyze/takara-human-rna-bcr-umi-smarter.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml b/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml index c077b159f..a8ef93457 100644 --- a/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml +++ b/regression/presets/analyze/takara-human-rna-bcr-umi-smartseq.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml b/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml index afc88d04a..9a286441a 100644 --- a/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml +++ b/regression/presets/analyze/takara-human-rna-tcr-smarter.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml b/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml index 473fffb96..61ea2407e 100644 --- a/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml +++ b/regression/presets/analyze/takara-human-rna-tcr-umi-smarter-v2.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml b/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml index 473fffb96..61ea2407e 100644 --- a/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml +++ b/regression/presets/analyze/takara-human-rna-tcr-umi-smartseq.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml b/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml index a9a026437..57a411957 100644 --- a/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml +++ b/regression/presets/analyze/takara-human-tcr-V1-cdr3.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml b/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml index afc88d04a..9a286441a 100644 --- a/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml +++ b/regression/presets/analyze/takara-human-tcr-V1-full-length.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml b/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml index 2fbb774f9..46847d5b1 100644 --- a/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml +++ b/regression/presets/analyze/takara-human-tcr-V2-cdr3.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml b/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml index 473fffb96..61ea2407e 100644 --- a/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml +++ b/regression/presets/analyze/takara-human-tcr-V2-full-length.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml b/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml index 63887c15b..850818ad7 100644 --- a/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml +++ b/regression/presets/analyze/takara-mouse-bcr-cdr3.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-mouse-bcr-full-length.yaml b/regression/presets/analyze/takara-mouse-bcr-full-length.yaml index f479b0644..adb35ef36 100644 --- a/regression/presets/analyze/takara-mouse-bcr-full-length.yaml +++ b/regression/presets/analyze/takara-mouse-bcr-full-length.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml b/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml index f479b0644..adb35ef36 100644 --- a/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml +++ b/regression/presets/analyze/takara-mouse-rna-bcr-smarter.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-mouse-rna-bcr-umi-smarseq.yaml b/regression/presets/analyze/takara-mouse-rna-bcr-umi-smarseq.yaml index acbf4b065..fd32b62bd 100644 --- a/regression/presets/analyze/takara-mouse-rna-bcr-umi-smarseq.yaml +++ b/regression/presets/analyze/takara-mouse-rna-bcr-umi-smarseq.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml b/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml index f479b0644..adb35ef36 100644 --- a/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml +++ b/regression/presets/analyze/takara-mouse-rna-tcr-smarter.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-mouse-rna-tcr-umi-smarseq.yaml b/regression/presets/analyze/takara-mouse-rna-tcr-umi-smarseq.yaml index 240e35273..e79af36a9 100644 --- a/regression/presets/analyze/takara-mouse-rna-tcr-umi-smarseq.yaml +++ b/regression/presets/analyze/takara-mouse-rna-tcr-umi-smarseq.yaml @@ -413,72 +413,72 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml b/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml index 63887c15b..850818ad7 100644 --- a/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml +++ b/regression/presets/analyze/takara-mouse-tcr-cdr3.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-mouse-tcr-full-length.yaml b/regression/presets/analyze/takara-mouse-tcr-full-length.yaml index f479b0644..adb35ef36 100644 --- a/regression/presets/analyze/takara-mouse-tcr-full-length.yaml +++ b/regression/presets/analyze/takara-mouse-tcr-full-length.yaml @@ -331,38 +331,38 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: OverlappedReadsMoreBetter - upper: 0.9 - middle: 0.8 + upper: 0.7 + middle: 0.6 label: Overlapped paired-end reads diff --git a/regression/presets/analyze/takara-sc-human-rna-tcr-smarter.yaml b/regression/presets/analyze/takara-sc-human-rna-tcr-smarter.yaml index 2de3161a2..e83bb3668 100644 --- a/regression/presets/analyze/takara-sc-human-rna-tcr-smarter.yaml +++ b/regression/presets/analyze/takara-sc-human-rna-tcr-smarter.yaml @@ -477,38 +477,38 @@ exportCloneGroups: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering - type: CellBarcodesWithFoundGroups - upper: 0.9 - middle: 0.8 + upper: 0.75 + middle: 0.6 label: Cell barcodes used in result groups diff --git a/regression/presets/analyze/test-gf-intersection.yaml b/regression/presets/analyze/test-gf-intersection.yaml index e285fd8bd..90cec413a 100644 --- a/regression/presets/analyze/test-gf-intersection.yaml +++ b/regression/presets/analyze/test-gf-intersection.yaml @@ -414,68 +414,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml b/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml index e6d3889c7..2ab546909 100644 --- a/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml +++ b/regression/presets/analyze/test-mikelov-et-al-2021-with-contigs.yaml @@ -437,68 +437,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml b/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml index b1acdb73e..41e73a69b 100644 --- a/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml +++ b/regression/presets/analyze/test-mikelov-et-al-2021-without-contigs.yaml @@ -436,68 +436,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/test-tag-from-header.yaml b/regression/presets/analyze/test-tag-from-header.yaml index 652398c26..f2996b18d 100644 --- a/regression/presets/analyze/test-tag-from-header.yaml +++ b/regression/presets/analyze/test-tag-from-header.yaml @@ -335,34 +335,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml b/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-bcr-oncomine-pan-clonality.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml index 6d1e0d9cd..629a541c0 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr1-j.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml index c0b3177ec..c5006304b 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr2-j.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-fr3-j.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml index 4a0e96d5f..dbd90c9bb 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-sr.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml index c409b4dbd..3f57dc8b0 100644 --- a/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-igh-oncomine-v-leader-j.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-dna-tcr-oncomine-pan-clonality.yaml b/regression/presets/analyze/thermofisher-human-dna-tcr-oncomine-pan-clonality.yaml index 5f5b97159..c475c798b 100644 --- a/regression/presets/analyze/thermofisher-human-dna-tcr-oncomine-pan-clonality.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-tcr-oncomine-pan-clonality.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-dna-trb-oncomine-sr.yaml b/regression/presets/analyze/thermofisher-human-dna-trb-oncomine-sr.yaml index 4a0e96d5f..dbd90c9bb 100644 --- a/regression/presets/analyze/thermofisher-human-dna-trb-oncomine-sr.yaml +++ b/regression/presets/analyze/thermofisher-human-dna-trb-oncomine-sr.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-lr.yaml b/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-lr.yaml index 66b0aca3c..27a4231e5 100644 --- a/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-lr.yaml +++ b/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-lr.yaml @@ -334,34 +334,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-sr.yaml b/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-sr.yaml index 4a0e96d5f..dbd90c9bb 100644 --- a/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-sr.yaml +++ b/regression/presets/analyze/thermofisher-human-rna-igh-oncomine-sr.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-lr.yaml b/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-lr.yaml index 65cf00502..b6421793e 100644 --- a/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-lr.yaml +++ b/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-lr.yaml @@ -331,34 +331,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-sr.yaml b/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-sr.yaml index 4a0e96d5f..dbd90c9bb 100644 --- a/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-sr.yaml +++ b/regression/presets/analyze/thermofisher-human-rna-trb-oncomine-sr.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-mouse-dna-igh-ampliseq-sr.yaml b/regression/presets/analyze/thermofisher-mouse-dna-igh-ampliseq-sr.yaml index b2fa0f9b8..a67bc16a1 100644 --- a/regression/presets/analyze/thermofisher-mouse-dna-igh-ampliseq-sr.yaml +++ b/regression/presets/analyze/thermofisher-mouse-dna-igh-ampliseq-sr.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-mouse-dna-tcb-ampliseq-sr.yaml b/regression/presets/analyze/thermofisher-mouse-dna-tcb-ampliseq-sr.yaml index b2fa0f9b8..a67bc16a1 100644 --- a/regression/presets/analyze/thermofisher-mouse-dna-tcb-ampliseq-sr.yaml +++ b/regression/presets/analyze/thermofisher-mouse-dna-tcb-ampliseq-sr.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-mouse-rna-igh-ampliseq-sr.yaml b/regression/presets/analyze/thermofisher-mouse-rna-igh-ampliseq-sr.yaml index b2fa0f9b8..a67bc16a1 100644 --- a/regression/presets/analyze/thermofisher-mouse-rna-igh-ampliseq-sr.yaml +++ b/regression/presets/analyze/thermofisher-mouse-rna-igh-ampliseq-sr.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/thermofisher-mouse-rna-tcb-ampliseq-sr.yaml b/regression/presets/analyze/thermofisher-mouse-rna-tcb-ampliseq-sr.yaml index b2fa0f9b8..a67bc16a1 100644 --- a/regression/presets/analyze/thermofisher-mouse-rna-tcb-ampliseq-sr.yaml +++ b/regression/presets/analyze/thermofisher-mouse-rna-tcb-ampliseq-sr.yaml @@ -303,34 +303,34 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml b/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml index 101c0548b..8a5108c06 100644 --- a/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml +++ b/regression/presets/analyze/vergani-et-al-2017-cdr3.yaml @@ -410,68 +410,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering diff --git a/regression/presets/analyze/vergani-et-al-2017-full-length.yaml b/regression/presets/analyze/vergani-et-al-2017-full-length.yaml index 8acaf0892..45c20e4c6 100644 --- a/regression/presets/analyze/vergani-et-al-2017-full-length.yaml +++ b/regression/presets/analyze/vergani-et-al-2017-full-length.yaml @@ -410,68 +410,68 @@ exportClones: qc: checks: - type: SuccessfullyAlignedReads - upper: 0.85 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Successfully aligned reads - type: OffTargetReads - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Off target (non TCR/IG) reads - type: ReadsWithNoVOrJHits - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no V or J hits - type: AlignmentsWithNoAssemblingFeature - upper: 0.15 - middle: 0.05 + upper: 0.3 + middle: 0.15 label: Alignments without assembling feature - type: ReadsWithNoBarcode - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Reads with no barcode - type: ReadsDroppedInTagRefinement - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags error correction and filtering - type: TagArtificialDiversityEliminated tag: UMI - upper: 0.5 - middle: 0.3 + upper: 0.7 + middle: 0.5 label: UMIs artificial diversity eliminated - type: ReadsDroppedInTagCorrection tag: UMI - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in UMI error correction and whitelist - type: ReadsDroppedInTagFiltering - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Reads dropped in tags filtering - type: TagGroupsWithNoAssemblingFeature - upper: 0.2 - middle: 0.1 + upper: 0.4 + middle: 0.2 label: Tag groups with no assembling feature - type: TagGroupsWithMultipleConsensuses - upper: 0.1 - middle: 0.01 + upper: 0.2 + middle: 0.05 label: Barcode collisions in clonotype assembly - type: UnassignedAlignments - upper: 0.1 - middle: 0.05 + upper: 0.25 + middle: 0.15 label: Unassigned alignments in clonotype assembly - type: ReadsUsedInClonotypes - upper: 0.9 - middle: 0.7 + upper: 0.7 + middle: 0.5 label: Reads used in clonotypes - type: AlignmentsDroppedLowQuality - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped due to low sequence quality - type: ClonesDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Clones dropped in post-filtering - type: AlignmentsDroppedInPostFiltering - upper: 0.05 - middle: 0.01 + upper: 0.15 + middle: 0.05 label: Alignments dropped in clones post-filtering