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
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
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