how to get a read sequence from reference genome

Question

[zhangdengwei]

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

[Nicolas Rosewick]

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

[zhangdengwei]

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

[GenoMax]

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.

[zhangdengwei]

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