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getzlab / rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization
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Intergenic regions #53

Closed ramyar1993 closed 3 years ago

ramyar1993 commented 3 years ago

Hi! Thanks for this tool. I have a lot of reads that align to intergenic regions. I was wondering if there is there a way that I can subset these reads for further analysis?

Thanks!

agraubert commented 3 years ago

Unfortunately, RNA-SeQC does not offer a way to subset reads like that, but you should be able to use bedtools to filter your bam to only include intergenic reads