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rMATS.smk

Snakemake workflow for differential RNA splicing analysis using rMATS.

Note

Please make sure that you have Singularity and Snakemake installed on your system and cloned the SnakeNgs repository.

Workflow

rMATS.smk rulegraph

The rulegraph was created by snakevision.

  1. Parse the experiment table to create the sample list.
  2. Run rMATS with --novelSS and the parameters specified in the config.yaml file.

Usage

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snakemake -s /path/to/SnakeNgs/snakefile/rMATS.smk \
--configfile /path/to/config.yaml \
--cores <int> \
--use-singularity \
--rerun-incomplete

config.yaml should contain the following information:

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workdir: /path/to/output
experiment_table: /path/to/experiment_table.tsv
gtf: /path/to/reference_transcriptome.gtf # Use unzipped GTF file

# rMATS
layout: paired # single or paired
readLength: 101 # Read length of the RNA-seq data
cstat: 0.1 # Cutoff for the statistical test
anchorLength: 6 # Anchor length for the reads
mil: 0 # Minimum intron length
mel: 10000 # Maximum exon length
  • /path/to/output is the directory where the output files will be saved.
  • /path/to/experiment_table.tsv is a tab-separated file, which is same as the one used in Shiba.
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sample  bam group
sample1 /path/to/sample1.bam    Ref
sample2 /path/to/sample2.bam    Ref
sample3 /path/to/sample3.bam    Ref
sample4 /path/to/sample4.bam    Alt
sample5 /path/to/sample5.bam    Alt
sample6 /path/to/sample6.bam    Alt

The group column must be specified as Ref or Alt. This workflow will perform the differential splicing analysis between the two groups.

  • /path/to/reference_transcriptome.gtf is the reference transcriptome in GTF format (e.g. Homo_sapiens.GRCh38.106.gtf for human transcriptome). Note that the GTF file should be unzipped.

Docker image used in the workflow