Question: how to get a read sequence from reference genome
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gravatar for zhangdengwei
10 months ago by
zhangdengwei50
zhangdengwei50 wrote:

hi, If I have the coordinate and length of a read, how can I fastly get its sequence from the reference genome? Thanks!!!

sequence • 202 views
ADD COMMENTlink written 10 months ago by zhangdengwei50

How To Use Coordinates In Order To Extract Sequences In Fasta File?

ADD REPLYlink written 10 months ago by Nicolas Rosewick8.7k

Yes! I want to use the coordinates of each reads in a bam or sam file to extract its corresponding sequence on reference genome.

ADD REPLYlink written 10 months ago by zhangdengwei50

I want to use the coordinates of each reads in a bam or sam file

You actually want coordinates of the hit that read has in the reference. This would require some manipulation of your alignment file (e.g. extract the reference chromosome name and the start of the hit). Then you could use that information to extract the relevant sequence from the reference.

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax78k

yes, thanks! That's what I want to ask. And is there any python module which can handle this problem quickly?

ADD REPLYlink written 10 months ago by zhangdengwei50
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