Achieving equivalent of -m mode for Bowtie2
Bowtie had a reporting mode -m, which, according to to the documentation, would "Suppress all alignments for a particular read or pair if more than <int> reportable alignments exist for it."
Is there a relatively simple/fast way to achieve this type of filtering for Bowtie2?
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This is an old answer so it may no longer be applicable. Take a look to check for yourself: A: Bowtie2, -M Alignment/Reporting Mode
Hi genomax. This isn't quite what I'm trying to do. My goal isn't only to keep unique alignments, but to exclude alignments with <int> number of reported alignments, like the -m mode in Bowtie.