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Old 01-30-2013, 09:01 PM   #1
says_anova
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Default generate fasta file from chipseq peaks

Hi all, hope someone has tried this before:

I have a collection of peaks from chipseq data. For each peak, I have the chr#, start position, and stop position. I'd like to generate a fasta file that contains the sequences from hg19 that correspond to each peak (one peak per line). Seems like there should be a tool out there to do this but my frantic googling is coming up short.

Advice??
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Old 01-30-2013, 11:56 PM   #2
balaji
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Could you explain, What do you want to do with the fasta sequence of each peak and for how many peaks you want to extract the fasta sequences.

an example http://genome.ucsc.edu/cgi-bin/das/h...r5:91000,91050

or see
http://www.biostars.org/p/7481/
http://www.biostars.org/p/6156/

and probably there are many more

Last edited by balaji; 01-31-2013 at 12:13 AM.
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Old 01-31-2013, 12:52 AM   #3
dariober
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Quote:
Originally Posted by says_anova View Post
Hi all, hope someone has tried this before:

I have a collection of peaks from chipseq data. For each peak, I have the chr#, start position, and stop position. I'd like to generate a fasta file that contains the sequences from hg19 that correspond to each peak (one peak per line). Seems like there should be a tool out there to do this but my frantic googling is coming up short.

Advice??
Hi- Have a look at fastaFromBed in BEDtools. You should be able to do something like:

Code:
fastaFromBed -fi hg19.fasta -bed mypeaks.bed -fo mypeaks.fasta
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Old 01-31-2013, 08:40 AM   #4
says_anova
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Thanks dariober! This looks like it'll do just what I need.

And thanks for the links, balaji, they're also helpful.

Update: yup, fastaFromBed did the trick!

Last edited by says_anova; 01-31-2013 at 09:09 PM.
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