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Old 07-16-2013, 02:48 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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Yeah, have a look at this thread on Biostars for some example commands. Allegedly, you can also use cmpfastq, which is a perl script, to do this too (I've never used this so I can't say that it works properly).

In the future, use a trimmer that handles both reads of a pair at once so you can avoid these issues.
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