Computes a series of quality control metrics for RNA-seq data.


Path to BWA, which should be set if it’s not in your path and BWArRNA is used.

Use an on the fly BWA alignment for estimating rRNA content. The value should be the rRNA reference fasta. If this flag is absent, rRNA estimation will be based upon the rRNA transcript intervals provided in the GTF (a faster but less robust method).

GCT file for expression correlation comparison. Note, that

This is a companion discussion topic for the original entry at quay.io/cancercollaboratory/dockstore-tool-rnaseqc