Question: Retrieve Sequence Near Snp
0
gravatar for omicj
5.7 years ago by
omicj60
San Diego
omicj60 wrote:

Hi all

I try to retrieve the sequence near SNP I found from sequencing data. Is there any efficient way to do that?

Thanks Jay

bioinformatics snp • 1.2k views
ADD COMMENTlink modified 5.7 years ago by Devon Ryan89k • written 5.7 years ago by omicj60
2

What organism? How much sequence around/near your SNP? What do you want to do with it after you have it?

ADD REPLYlink written 5.7 years ago by Alex Paciorkowski3.3k
1
gravatar for Devon Ryan
5.7 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

If you have a copy of the genome (I'm assuming that this is your own sequencing data, in which case you likely would), just use "samtools faidx chromosome:region.start-region.end".

ADD COMMENTlink written 5.7 years ago by Devon Ryan89k
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