Question: Fasta file from a gff file
1
gravatar for ahmedferoz20
23 months ago by
ahmedferoz2010
ahmedferoz2010 wrote:

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.

genome gene • 838 views
ADD COMMENTlink modified 23 months ago by Kevin Blighe65k • written 23 months ago by ahmedferoz2010
1

Look at bedtools or bedops.

ADD REPLYlink modified 23 months ago • written 23 months ago by h.mon31k

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

ADD REPLYlink written 23 months ago by ahmedferoz2010

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 REPLYlink written 23 months ago by Joe18k
1
gravatar for Kevin Blighe
23 months ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

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 COMMENTlink written 23 months ago by Kevin Blighe65k
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