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Old 09-08-2014, 04:18 PM   #4
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

I don't see an option for it, though you can split the output with samtools into mapped and unmapped reads.

Alternatively, BBMap supports unlimited reference size and also separate files for mapped and unmapped reads, using the "outm=" and "outu=" flags. The output can be in sam or other formats, depending on the file extension.
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