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Old 07-29-2016, 10:48 AM   #3
Location: Alaska

Join Date: May 2009
Posts: 20

thanks for your response. Yes, most people doing seqCap are using transcriptome data for bait design. But those people are interested in phylogenetics. We're interested in within-species diversity (or btw 2 very closely related species), so we don't really want conserved regions - though with 5-10,000 baits, even conserved regions would probably give enough snps to see if the 2 species are different from each other.
My husband thinks that blasting all of the unassembled reads is unreasonable bc there are millions of reads. but metagenomics people seem to do that
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