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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 BAM files as input to the WASP subworkflow #71

Open aryarm opened 3 years ago

aryarm commented 3 years ago

The WASP subworkflow requires RNA-seq FASTQ files as input. But what if the alignment step has already been performed, and the user only has BAM files, instead?

We could automatically skip the first mapping step and go right to find_intersecting_SNPs. To ensure the second mapping step is performed identically to the first, we can add a config option allowing the user to provide the argument for the second mapping step or we could try to take it from the @PG tags in the BAM header.

aryarm commented 3 years ago

see a61b7bc and f3f9dad for a new aln_cmd config option! I decided not to take it automatically from the header because I figured that would get super messy.