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utia-gc / rnaseq

A Nextflow pipeline for RNA-seq analysis based on utia-gc/ngs.
https://utia-gc.github.io/rnaseq/
MIT License
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STAR throws out unmapped reads #29

Open trev-f opened 2 hours ago

trev-f commented 2 hours ago

STAR doesn't output unmapped reads in the BAM file. This causes unexpected results in the QC. The tools that report stats on the BAM files make it seemed that 100% of the reads are mapped, but this is just because the unmapped reads never make it into the SAM file written by STAR.

I believe this can be remedied by using the STAR option --outSAMunmapped'Within KeepPairs. Consider adding this to the default arguments.

trev-f commented 2 hours ago

Presumably this is a bug that should be fixed at the level of utia-gc/ngs