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Whippet.smk

Snakemake workflow for differential RNA splicing analysis using Whippet.

Note

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

Workflow

Whippet.smk rulegraph

The rulegraph was created by snakevision.

  1. Quantify Percent Spliced In (PSI) values using Whippet quant.
  2. Differential splicing analysis using Whippet delta.

Usage

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snakemake -s /path/to/SnakeNgs/snakefile/Whippet.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
whippet_index: /path/to/whippet_index/graph.jls
  • /path/to/output is the directory where the output files will be saved.
  • /path/to/experiment_table.tsv is a tab-separated file containing the following information:
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sample  fastq   group
sample1 /path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz   Ref
sample2 /path/to/sample2_R1.fastq.gz,/path/to/sample2_R2.fastq.gz   Ref
sample3 /path/to/sample3_R1.fastq.gz,/path/to/sample3_R2.fastq.gz   Ref
sample4 /path/to/sample4_R1.fastq.gz,/path/to/sample4_R2.fastq.gz   Alt
sample5 /path/to/sample5_R1.fastq.gz,/path/to/sample5_R2.fastq.gz   Alt
sample6 /path/to/sample6_R1.fastq.gz,/path/to/sample6_R2.fastq.gz   Alt

The fastq column should contain the paths to the FASTQ files for each sample. R1 and R2 files should be separated by a comma. The group column must be specified as Ref or Alt. This workflow will perform the differential splicing analysis between the two groups.

  • /path/to/whippet_index/graph.jls is the Whippet index file.

Docker image used in the workflow