picard CollectRnaSeqMetrics gene coverage

Question

[noodle]

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.

[Pierre Lindenbaum]

exclude or include rRNA?

you provide the reflat file. It's your choice to select the transcripts you want.

https://broadinstitute.github.io/picard/command-line-overview.html

REF_FLAT (File) Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required.

[noodle]

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

Answer 1

[noodle]

In case this comes up in a search - it seems that anything that is passed to --RIBOSOMAL_INTERVALS will be excluded from the 'mRNA' analysis of this tool (gene coverage does not include rRNA as long as rRNA is defined in --RIBOSOMAL_INTERVALS even if it is included in the refFlat)