Entering edit mode
7.2 years ago
emblake
▴
90
Is there an ENSEMBL tRNA, rRNA masked GTF file available for GRCh38.p7? If not, would someone kindly provide info on creating one? I'm using STAR to align PE RNA-seq data and featureCounts for read counting. Thank you!
Can you not ignore counts for those line items afterwards?
Or use the default GTF and filter out lines you don't like?
Yes, I'm just not sure how to ignore those counts. Would something like
grep -wv rRNA,tRNA Homo_sapiens.GRCh38.87.gtf | Homo_sapiens.GRCh38.87.masked.gtf
work to generate a masked GTF file for input into featureCounts?You will have to redirect
>
instead of|
but that should work. A small nitpick but that is not a masked file but a file without lines containing RNA entries.Thanks! How would I do the latter?
This should do it.
grep -wv rRNA,tRNA Homo_sapiens.GRCh38.87.gtf > Homo_sapiens.GRCh38.87.noRNA.gtf
Got it. Is there a better or recommended alternative to masking/removing RNA entries than generating a new GTF file?