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Old 05-08-2017, 05:52 PM   #16
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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In that case, mapping the co-normalized reads and assembling the unmapped portion should be fine. I recommend with this strategy that if you have a pair in which only one read maps, to use both of for assembly, since presumably at least one was not assembled, and the other may have mapped to something that it did not actually come from. Of course, if that generates too much data to assemble, you can also just discard half-mapped pairs.
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