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Old 02-09-2015, 09:28 PM   #10
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Yes, it can. BBNorm will (by default, it can be changed) discard pairs based on the depth of the lower mate, so if read 1 has high coverage and read 2 has low coverage, the pair will not be discarded. If both are high depth, they will be discarded.
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