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Old 04-29-2011, 06:16 AM   #6
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Location: St. Louis

Join Date: Dec 2010
Posts: 535

@Robby: We sequence with the HiSeq and I get generally ~90-100 million reads. We map to the whole genome using novoalign but that shouldn't be a determining factor regarding how many duplicate reads there are. I have no idea why you are getting so many duplicates or, even more interestingly, why you would get less duplicates with the GAIIx. I've generally started with 3-4 ug DNA and done 7-8 PCR cycles pre-hybridization (around 12 after hybridization).
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