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Gtfcuff to extract only intergenic transcripts after Gffcompare #2

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julienvibert opened this issue Nov 20, 2019 · 0 comments
Open

Gtfcuff to extract only intergenic transcripts after Gffcompare #2

julienvibert opened this issue Nov 20, 2019 · 0 comments

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@julienvibert
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Hi,

Thanks for the wonderful tools!
I was wondering: when using Scallop, we have the command (Step 4 of tutorial):
gtfcuff puniq gffall.scallop.gtf.tmap scallop.gtf reference.gtf unique.gtf
which is used to extract "uniquely expressed transcripts" after having run the tool Gffcompare, is it possible to extract only the transcripts classified by Gffcompare as "u" (unknown, intergenic) with Gtfcuff?
Thanks a lot for your help!

Best,

Julien
@julienvibert julienvibert changed the title Gtcuff to extract only intergenic transcripts after Gffcompare Gtfcuff to extract only intergenic transcripts after Gffcompare Nov 20, 2019
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