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Old 07-23-2015, 08:34 AM   #3
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Hi Vicente,

It's much better to interleave them, because that way you use all the kmers in both files.

For input and output in two files, though, you can set "in1" and "in2": in1=r1.fq in2=r2.fq oute1=ext1.fq oute2=ext2.fq mode=extend extendright=100 ecc=t

The "oute" and "out" flags are kind of synonymous, but kind of not (there is no out2); I'll rectify that in the next release and get rid of "oute" as it's confusing. "el" and "er" are short for "extendleft" and "extendright", and there's no reason to extend left if all you want is to make the reads overlap, but it is useful if you want longer reads so that you can assemble with a larger K, or use a string-graph assembler, or whatever.
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