ENSEMBL masked GTF file?

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7.3 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!

RNA-Seq ensembl • 2.4k views

ADD COMMENT • link 7.3 years ago by emblake ▴ 90

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Can you not ignore counts for those line items afterwards?

ADD REPLY • link 7.3 years ago by GenoMax 141k

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

ADD REPLY • link 7.3 years ago by WouterDeCoster 47k

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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 REPLY • link 7.3 years ago by emblake ▴ 90

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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 REPLY • link 7.3 years ago by GenoMax 141k

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Thanks! How would I do the latter?

ADD REPLY • link 7.3 years ago by emblake ▴ 90

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

ADD REPLY • link 7.3 years ago by GenoMax 141k

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

ADD REPLY • link 7.3 years ago by emblake ▴ 90

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