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aryarm / as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq
MIT License
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allow gzipped FASTAs and GTFs when using STAR #64

Open aryarm opened 3 years ago

aryarm commented 3 years ago

STAR by default does not support gzipped FASTAs and GTFs. So the WASP subworkflow just fails if the user provides files that are gzipped. But it would be great if the pipeline automatically handled the gzipped case. Here are some potential workarounds.

aryarm commented 3 years ago

I have uncommited changes for this that still need to be tested