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Old 06-02-2012, 04:26 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
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It does depend on the quality of your reference but I would say the first. I see no reason to do a de-novo assembly, especially for SNP discovery, when you can do an mapping instead. De-novo will always give worse and more questionable results.

As for how to determine which ones are correct ... back to the lab you go! Independent verification via different methodology is the definitive proof. Oh, you can also take your sequencing results and apply statistical filters to it and list the SNPs that fall into, say, p<0.05 but where is the fun in that?
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