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SUPPA2_diffSplice.smk

Snakemake workflow for differential RNA splicing analysis using SUPPA2.

Note

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

Workflow

SUPPA2_diffSplice.smk rulegraph

The rulegraph was created by snakevision.

  1. Quantify transcript abundances (TPM) for each sample using salmon.
  2. Merge the quantification results into a single file.
  3. Make a list of alternative splicing events using SUPPA2 generateEvents.
  4. Quantify Percent Spliced In (PSI) values using SUPPA2 psiPerEvent.
  5. Separate the PSI values into two groups.
  6. Separate the TPM values into two groups.
  7. Differential splicing analysis using SUPPA2 diffSplice.

Usage

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snakemake -s /path/to/SnakeNgs/snakefile/SUPPA2_diffSplice.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
salmon_index: /path/to/salmon_index
gtf: /path/to/reference_transcriptome.gtf
  • /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/salmon_index is the directory containing the salmon index.
  • /path/to/reference_transcriptome.gtf is the reference transcriptome in GTF format (e.g. Homo_sapiens.GRCh38.106.gtf for human transcriptome).

Docker image used in the workflow