Extract transcripts overlaping given coordinates with gffread (basic usage question)

[Vicho Deivis]

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

[GenoMax]

You could potentially trim your gff file to contain just the chromosome you want.

[Vicho Deivis]

As a last resort yes. But I'm trying to do a pipeline as clean as possible,

[GenoMax]

Use -r [<chr>:]<start>..<end> format in your command.

[Vicho Deivis]

Now it works. Thanks!