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Old 11-26-2018, 11:58 AM   #1
Vicho Deivis
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Default Extract transcripts overlaping given coordinates with gffread (basic usage question)

Hello, sorry if its already answered but I'm having problems using gffread.

I have a list of short regions of interest (20-50pb) and I want to extract all features that overlap with this region. So far I have tried gffreead with the -r option with the following usage but I've been unable to indicate the chromosome I want.

-> gffread -r start..end annotation.gff3 -o Test.results

Thanks for your time
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Old 11-26-2018, 12:05 PM   #2
GenoMax
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You could potentially trim your gff file to contain just the chromosome you want.
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Old 11-26-2018, 12:10 PM   #3
Vicho Deivis
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As a last resort yes. But I'm trying to do a pipeline as clean as possible,
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Old 11-26-2018, 12:15 PM   #4
GenoMax
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Use -r [<chr>:]<start>..<end> format in your command.
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Old 11-26-2018, 12:22 PM   #5
Vicho Deivis
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Now it works. Thanks!
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