Question: ENSEMBL masked GTF file?
0
gravatar for emblake
2.8 years ago by
emblake50
United States
emblake50 wrote:

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!

rna-seq ensembl • 1.3k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by emblake50
1

Can you not ignore counts for those line items afterwards?

ADD REPLYlink written 2.8 years ago by genomax74k

Or use the default GTF and filter out lines you don't like?

ADD REPLYlink written 2.8 years ago by WouterDeCoster42k

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?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by emblake50

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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax74k

Thanks! How would I do the latter?

ADD REPLYlink written 2.8 years ago by emblake50

This should do it. grep -wv rRNA,tRNA Homo_sapiens.GRCh38.87.gtf > Homo_sapiens.GRCh38.87.noRNA.gtf

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax74k

Got it. Is there a better or recommended alternative to masking/removing RNA entries than generating a new GTF file?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by emblake50
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