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Old 05-08-2017, 04:00 PM   #14
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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If you plan to normalize the reads after mapping but before assembly anyway, then yes, it's logical to just map with the normalized reads... but only if the reads were normalized together (which they probably weren't). If they were normalized independently, you need to either combine them all, then normalize, then map, or map, then combine them all, then normalize. Normalizing independently will lose the low-coverage part of each library (depending on your settings) that could still be assembled once the libraries are combined.
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