Sleuth #11
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…e running R scripts
…ler dataset has been generated
…le from kallisto_quant
rehamFatima
reviewed
Jun 5, 2018
docs/test_data/testData_Sleuth.rst
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| .. code-block:: none | ||
| :linenos: | ||
| # Extract the original reads from teh FASTQ files |
process_sleuth.py
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| class process_sleuth(Workflow): | ||
| """ | ||
| Functions for processing Chip-Seq FastQ files. Files are the aligned, |
process_sleuth.py
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| metadata : dict | ||
| Input file meta data associated with their roles | ||
| kallisto_tar : str |
scripts/install_sleuth.R
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| source("http://bioconductor.org/biocLite.R") | ||
| if(!require("rhdf5")) biocLite("rhdf5") | ||
| if(!require("devtools")) install.packages("devtools") | ||
| if(!require("sleuth")) devtools::install_github("pachterlab/sleuth") No newline at end of file |
| "file_path": "tests/data/kallisto.run_info.json", | ||
| "file_path": "tests/data/kallisto.Human.ERR030872.tar.gz", | ||
| "data_type": "data_rna_seq", | ||
| "compressed": "null" |
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(Q) . What exactly is the compressed tag for ?
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Indicate if the file is compressed or not.
tidy_data.sh
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| fi | ||
| done | ||
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| # Added to remove the Sleuth results folder due to nexted structure |
tool/kallisto_quant.py
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| ), | ||
| "run_info_file": Metadata( | ||
| "kallisto_tar_file": Metadata( | ||
| data_type="data_ranseq", |
| } | ||
| } | ||
| ] | ||
| } No newline at end of file |
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This is fine as it is a JSON file
tool/sleuth.py
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| class sleuthTool(Tool): # pylint: disable=invalid-name | ||
| """ | ||
| Tool for peak calling for iDamID-seq data |
tool/sleuth.py
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| def run(self, input_files, input_metadata, output_files): | ||
| """ | ||
| The main function to run Sleuth over a set of RNA-seq experiments | ||
| nalysed using Kallisto to identify differentially expressed genes. |
pabloacera
approved these changes
Jun 12, 2018
…o that any dataset/expt info is also retained
…of the files metadata
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Awaiting confirmation about the method for passing the parameters to the RNA-seq pipeline and Sleuth before merging. |
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This is a new tools for the analysis of differential gene expression.
It has required changes to the original process_rnaseq pipeline for the packaging of the results as well as new pipelines and tools.