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Published 20 hours ago • verified publisher icon hbctraining

add --validateMappings to salmon command

Open mistrm82 opened this issue 5 years ago • 1 comments

this is now running by default in bcbio, we should incorporate it with an explanation why.

Also Rory says:

"Also, I’ve been turning on quantitate_genome_alignments which uses the STAR alignments to quantitate with, rather than quantifying from the reads.

That is a bigger change though"

mistrm82 avatar Oct 29 '19 20:10 mistrm82

Also, we might want to check out the --writeMappings argument and the resulting SAM file

marypiper avatar Oct 30 '19 13:10 marypiper