Entering edit mode
18 months ago
joe
▴
470
Hi all,
Does anyone know if the normalized gene coverage statistics provided by picard CollectRnaSeqMetrics
exclude or include rRNA?
...I'd ask on the gatk website but the forum seems down for new posts.
you provide the reflat file. It's your choice to select the transcripts you want.
https://broadinstitute.github.io/picard/command-line-overview.html
Thanks, I guess more specifically I am also providing the
--RIBOSOMAL_INTERVALS
parameter, so I would expect that rRNA would be excluded but it's not clear...I guess I should just run with 2 refFlat files w & w/o rRNA and compare