how to do target mapping efficiently

[sadiexiaoyu]

Dear All,

I would like to align the reads to some target genome region (for example, the gene I am interested in in the reference genome). Is there any efficient way to do this kind of target mapping instead of align the reads to the whole genome? For example, maybe I can extract the target gene sequences I am interested in in the reference genome, and make a new file? Is that possible?


Thanks!

Best,

Sadiexiaoyu

[Brian Bushnell]

You could extract the target gene sequence and map to it, but it's more accurate to map to the whole genome to avoid mismapping of ambiguous reads.

[swbarnes2]

You can make a new reference containing only the target sequence, and align to that, and that would be faster.

But as Brian said, if you have reads that don't align there, you run the risk of forcing them to align to your target when they map better elsewhere.

[sadiexiaoyu]

You could extract the target gene sequence and map to it, but it's more accurate to map to the whole genome to avoid mismapping of ambiguous reads.

Ahha, yes, you are right!

[sadiexiaoyu]

You can make a new reference containing only the target sequence, and align to that, and that would be faster.

But as Brian said, if you have reads that don't align there, you run the risk of forcing them to align to your target when they map better elsewhere.

Yes, I agree with you. Thanks for the reply!