Making sense of single gene sequence

[SirMagnus]

I have sequenced whole genome using MiSeq (low coverage) - I am looking for a candidate deletion in just a single gene (in a specific exon). I don't have very good computer resources - which strategies would anyone recommend for mapping reads to just an abbreviated genomic region around an MSH gene?

I guess I am trying to ask whether it makes sense to map all reads to the reference genome or whether anyone has used other methods for mapping subsets only? Sorry for bad English

Thanks

Siri

[swbarnes2]

You can align to just the bit of reference sequence you want, but you will get more accurate mapping if you provide the aligner with the whole reference. What you don't want is an read that aligns perfectly on Chr 6 to be forced to align with two errors on Chr 1because you only gave it Chr 1 to align to.

After aligning to the whole genome, you can filter you .bam so that you are only looking the exact area you care about.