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Old 01-29-2014, 01:16 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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Correct, there's no option to tell bowtie2 to only report unique alignments. For bowtie2 (I should note that this is ONLY true for bowtie2), MAPQ scores of 0 and 1 indicate non-unique mapping, so you can filter by that (though not if you use "-k 1", since this only works when you have actual MAPQ values). Alternatively (also not when "-k 1" is used, but a bit more portable to other aligners), you can often just look for reads with "NH:i:1" auxiliary tags, though that's more work.
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