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Old 02-24-2015, 12:43 PM   #9
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695
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Hi Vicente,

The output will come out interleaved (alternating read1/read2) if the input was paired. There's currently not a way to make BBSplit write twin output files for the "basename" output streams (though I'll make a note to add that feature). You can de-interleave the output like this:

reformat.sh in=out_ecoli.fq out1=out_ecoli_r1.fq out2=out_ecoli_r2.fq

BBMap does not understand the "basename" flag so it doesn't work for splitting, but BBMap's "out", "outu", and "outm" all allow output of twin files using "out1" and "out2", etc.
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