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Old 03-06-2016, 09:05 PM   #31
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Oh... sorry, the explanation is a bit different here. By default BBNorm runs in 2-pass mode, which gives the best normalization. However, that generates temp files (which are later deleted). The final outputs are only from the second pass - reads discarded in the first pass would disappear completely.

For what you are doing I recommend this command: in=input_fq1.gz in2=input_fq2.gz zerobin=t prefilter=t target=1000 min=10 passes=1 ecc=t out1=bbnorm.fq1.gz out2=bbnorm.fq2.gz outt=excluded.fq.gz

Then the output numbers should add up as expected.
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