Merge pull request #39 from hexavier/master

drewjbeh · web-flow · commit a9750dc1f225 · 2023-02-08T16:18:07.000+01:00
Add documentation of SLAC algorithm
diff --git a/README.md b/README.md
@@ -21,6 +21,7 @@ This package is an automated analysis pipeline for the quantitation and analysis
 * Calculate tRNA differential expression with [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
 * Analyze functional tRNA pools and tRNA completeness via 3'-CCA analysis
 * Comprehensive modification quantification and misincorporation signature analysis
+* Detect coordination between pairs of modifications and modification-aminoacylation with [SLAC](https://doi.org/10.1093/nar/gkac1185) (SingLe-read Analysis of Crosstalks)
 
 ## Method strategy
 
@@ -72,6 +73,11 @@ An example command to run mim-tRNAseq may look as follows. This will run an anal
 ```
 The run should take around 15 minutes on a server using 15 processors (`--threads 15`: please update according to your server capabilities).
 
+To run the [SingLe-read Analysis of Crosstalks (SLAC)](https://doi.org/10.1093/nar/gkac1185) between tRNA modifications and aminoacylation, specify the optional argument `--crosstalks`. The run can take a few minutes longer depending on the number of processors.
+```bash
+	mimseq --species Hsap --cluster-id 0.97 --threads 15 --min-cov 0.0005 --max-mismatches 0.075 --control-condition HEK293T -n hg38_test --out-dir hg38_HEK239vsK562 --max-multi 4 --remap --remap-mismatches 0.05 --crosstalks sampleData_HEKvsK562.txt
+```
+
 ## Contact
 
 Please log all issues/suggestions on the mim-tRNAseq GitHub page: https://github.com/nedialkova-lab/mim-tRNAseq/issues
diff --git a/docs/img/slac.png b/docs/img/slac.png
diff --git a/docs/source/contact.rst b/docs/source/contact.rst
@@ -10,6 +10,8 @@ Authors
 
 Max Planck Institute for Biochemistry, Germany
 
+:Developer: Xavier Hernandez-Alias (Centre for Genomic Regulation, Spain), developed the SingLe-read Analysis of Crosstalks (SLAC).
+
 Contribute
 ^^^^^^^^^^
 
@@ -24,3 +26,4 @@ Behrens et al., 2021, High-resolution quantitative profiling of tRNA abundance a
 
 Behrens and Nedialkova, 2022, Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq. STAR Protocols. 3, 101579 (https://doi.org/10.1016/j.xpro.2022.101579)
 
+Hernandez-Alias et al., 2022, Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation. Nucleic Acids Research, gkac1185 (https://doi.org/10.1093/nar/gkac1185)
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -24,9 +24,11 @@ This package is a semi-automated analysis pipeline for the quantification and an
 * Calculate tRNA differential expression with DESeq2_.
 * Analyze functional tRNA pools and tRNA completeness via 3'-CCA analysis.
 * Comprehensive modification quantification and misincorporation signature analysis.
+* Detect coordination between pairs of modifications and modification-aminoacylation with SLAC_ (SingLe-read Analysis of Crosstalks).
 
 .. _GSNAP: http://research-pub.gene.com/gmap/
 .. _DESeq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
+.. _SLAC: https://doi.org/10.1093/nar/gkac1185
 
 
 Index
diff --git a/docs/source/intro.rst b/docs/source/intro.rst
@@ -33,3 +33,12 @@ Transcripts that are not deconvoluted are renamed to provide details on which tr
 
 
 .. image:: ../img/unsplitDeconv.png
+
+SingLe-read Analysis of Crosstalks
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Since v1.2.1, the SingLe-read Analysis of Crosstalks (SLAC; `Hernandez-Alias <https://doi.org/10.1093/nar/gkac1185>`_ et al., 2022, Nucleic Acids Research, gkac1185) has been incorporated in the mim-tRNA-seq software, which allows the detection of transcriptome-wide crosstalks between pairs of tRNA modifications and modification-aminoacylation.
+
+Because of its size, tRNA-seq produces reads that can cover the entire length of the tRNA; tRNA-seq also captures certain tRNA modifications as ‘misincorporations’ relative to the reference tRNA sequence, and the charging status by the 3'-CCA ends depending on the library construction protocol. SLAC considers all pairwise combinations modification-modification and modification-charging. For each pair, it determines the number of reads for: (i) both sites are modified/charged, (ii) site 1 is, site 2 is not modified/charged, (iii) site 1 is not, site 2 is modified/charged and (iv) both sites are not modified/charged. The analysis produces an odds ratio (OR) that informs whether the pair of modification-modification or modification-charging tend to appear together in the same read (OR > 1, stimulatory crosstalk) or tend to be exclusive of one another (OR < 1, inhibitory crosstalk), as well as calculates the significance of this interdependence using Fisher's exact test.
+
+.. image:: ../img/slac.png
diff --git a/docs/source/output.rst b/docs/source/output.rst
@@ -113,3 +113,9 @@ Various files describing the tRNA trascriptome of the genome of interest.
 	* `\*clusters.bed`: bed6 file for cluster parents. Only if clustering is enabled.
 	* `\*clusterInfo.txt`: Cluster parent-child relationship for every tRNA gene, with unique cluster number and size. Only if clustering is enabled.
 
+**single_read_data**
+
+Only generated if --crosstalks is specified. The analysis includes all modified sites based on misinc-thresh.
+
+* `*crosstalks.tsv`: Data table for all tRNA crosstalk analyses by `SLAC <https://doi.org/10.1093/nar/gkac1185>`_. Includes tRNA/cluster, pair of crosstalking positions, Fisher exact test p-value, odds ratio, contingency table with read counts, FDR-corrected p-value, and canonical tRNA position information (NAs indicate low-coverage positions). The odds ratio informs whether two modifications/charging tend to appear together in the same read (OR > 1) or tend to be exclusive of one another (OR < 1).
+
