constructing a reference

[nozzer]

Hi,

I need to align and call snps for a 14mb region of resequenced gDNA. I'm just thinking about the best way to construct my ref sequence. Exons, promoters,5' and 3' ends, conserved non-coding seqs and predicted alternative splicing sites have been selectively sequenced. Would the best approach be to just align against this whole section of hg18 using a gapped aligner as opposed to attempting to construct a ref sequence from parts of this region?

thanks in advance

[dnusol]

I´d suggest you align against the whole genome and then just focus on your region of interest. This way you probaly avoid genomic duplications.

HTH