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Old 12-18-2014, 01:50 PM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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BBDuk will do that. For example, if you want to remove phiX reads, and reads with average quality below 10:

bbduk.sh ref=phix.fasta k=31 maq=10 in=reads.fq out=good.fq outm=bad.fq

Passing reads go to out, and failing reads go to outm. I'm not sure whether you can do this with Trimmomatic; the manual seems to indicate that you can save pairs where one fails and the other doesn't, but does not seem to mention a way to catch all filtered reads.
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