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Old 09-11-2021, 05:40 AM   #688
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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@mewu3: Since paired-end reads are aligned together you should use a single "out=output.sam". If you wanted to capture unmapped reads into separate files then you would want to do that as "outu1=R1.unmapped.fq outu2=R2.unmapped.fq".

You may be able to write them out as an unmapped sam file "outu=unmapped.sam" but then again you should use only one output for that. This is untested.
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