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Fasta file from a gff file

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
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updated by Kevin Blighe Kevin Blighe • written by ahmedferoz20 • ahmedferoz20

Look at bedtools or bedops.

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written by h.mon h.mon

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

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written by ahmedferoz20 • ahmedferoz20

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

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written by Joe Joe

1 answer

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

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written by Kevin Blighe Kevin Blighe

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