Sequence mapping

[Poni]

Hi,
I want to map sequence reads into a reference gene. However, it's possible to have a higher number of SNPs and few insertions and/or deletions for this gene in the genome that I'm analyzing. May I please know which mapping software is suitable for this purpose and whether its useful to allow many mismatches?
Your advise is highly appreciated.

Poni

[TiborNagy]

I think there is no specific software for this job. Try BWA and decrease the mismatch penalty (-M).

[qiongyi]

Try BWA or bowtie2.

[Poni]

Thanks for the suggestions.
Poni

[Torst]

Hi,
I want to map sequence reads into a reference gene. However, it's possible to have a higher number of SNPs and few insertions and/or deletions for this gene in the genome that I'm analyzing. May I please know which mapping software is suitable for this purpose and whether its useful to allow many mismatches?

Is your reference a whole genome, or just a single gene?

Nearly all short read aligners trade sensitivity for speed. What you need is increase the sensitivity OR use a true dynamic programming aligner which implements Smith-Waterman or Needleman-Wunsch alignment. Tools which can do this are the FASTA 36 package (http://faculty.virginia.edu/wrpearson/fasta/), Exonerate with the affine model (http://www.ebi.ac.uk/~guy/exonerate/) and Needle/Water (http://emboss.sourceforge.net/).

Personally, I would use Shrimp 2.x (http://compbio.cs.toronto.edu/shrimp/) which does well with indels.

[Poni]

Dear Torst,
Thanks for this discriptive reply. my reference is a single gene.
I will try Shrimp 2.x and see.

Thanks
Poni