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picard CollectRnaSeqMetrics gene coverage

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.

picard gatk collectrnaseqmetrics
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written by noodle 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

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written by noodle noodle

1 answer

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)

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written by noodle noodle

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