/IsoformSwitches

Primary LanguageR

Snakemake License

Snakemake Workflow for Isoform Switches

This is a snakemake pipeline to detect isoform switches from RNASeq data. The pipeline is in progress. It uses IsoformSwitchAnalyzer tool so far. The pipeline detects alternative splicing and differential isoform switchs. In addition, it relies on some external sources to analyze the consequences of those switches, including coding potential, ORF similarity, Intron retention, etc.

Output Example

Gene Specific Plots

RNF2.png

Splicing Summary

splicingsummary.png

Consequence Enrichment::

consequencenrichment.png

Volcano Plots

volcanoplots.png

Gene Enrichment

genenrichment.png

Genome Wide

genomewide.png

Run the pipeline

snakemake -jn

where n is the number of cores for example for 10 cores use:

snakemake -j10

Use conda

For less froodiness, use conda:

snakemake -jn --use-conda

For example, for 10 cores use:

snakemake -j10 --use-conda

This will pull automatically the same versiosn of tools we used. Conda has to be installed in the system, in addition to snakemake.

Dry Run

For a dry run use:

snakemake -j1 -n

and to print command in dry run use:

snakemake -j1 -n -p

Use Corresponding configfile:

Just update your config file to include all your sample names, edit your interval.list file to include your intervals of interest, your path, etc for example:

snakemake -j1 --configfile config-WES.yaml

or:

snakemake -j1 configfile config-WGS.yaml

References

  1. Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Cancer Res. (2017)