Question

Fasta file from a gff file

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6.1 years ago

ahmedferoz20 ▴ 10

Hi, I have a GFF file and a genome sequence file in fasta format. I need to get a fasta file containing the sequence of 1 kb uspstream of each gene on the x chromosome?

I prefer linux scripts however, python code is fine too.

Really appreciate if anyone can help me.

gene genome • 2.2k views

ADD COMMENT • link updated 6.1 years ago by Kevin Blighe 88k • written 6.1 years ago by ahmedferoz20 ▴ 10

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Look at bedtools or bedops.

ADD REPLY • link 6.1 years ago by h.mon 35k

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Thanks h.mon. I am wondering is it working for gff file too?

ADD REPLY • link 6.1 years ago by ahmedferoz20 ▴ 10

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BioPython would make this very easy, though their support for GFF is limited. Brad Chapman built BCBio though which handles gff and is able to interface with BioPython nicely

ADD REPLY • link 6.1 years ago by Joe 21k

score 1 · Answer 1 · 2018-10-22

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6.1 years ago

Kevin Blighe 88k

Hey bro,

gffread can do this for you, and it is strand-specific. Take a look at the example here: A: Cufflinks gffread utility

To add 1000bp up and downstream of each gene, then just write a script that modifies the GFF input file. AWK should easily work, in this regard.

Kevin

ADD COMMENT • link 6.1 years ago by Kevin Blighe 88k