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Old 01-14-2013, 10:33 AM   #2
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Location: US

Join Date: Jan 2009
Posts: 392

How big are your inserts? Because even if <5% of reads were informative, that may be enough. A single lane on a HiSeq gives well over 100 million reads anymore, so if only 5% of reads are informative, that is still several million informative reads. Even if you have a couple hundred plasmids, you will have tens of thousands of 100 bp reads covering that.
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