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Old 06-29-2012, 10:16 AM   #1
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Default Not report promiscuous reads in bowtie

I was wondering if there is a way in bowtie to stop further alignment of short reads that have already mapped to more than a certain number of locations. Say I have a read that has aligned perfectly to 20 locations and I want bowtie to not align it further and stop processing it so that it does not waste any more time in trying to align these short promiscuous reads. Is there a way to do this in bowtie: not report/align reads that have aligned to more than say 10 locations?
Or any quick tool afterwards to delete these reads from the sam file?
thanks a lot in advance, any help will be greatly appreciated.
floydian_slip is offline   Reply With Quote
Old 06-30-2012, 12:57 PM   #2
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Hi- Isn't the -k option what your are looking for?
From bowtie2 manual:

-k <int>
In this mode, bowtie2 searches for at most <int> distinct, valid alignments for each read. The search terminates when it can't find more distinct valid alignments, or when it finds <int>, whichever happens first. All alignments found are reported in descending order by alignment score. The alignment score for a paired-end alignment equals the sum of the alignment scores of the individual mates. Each reported read or pair alignment beyond the first has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. For reads that have more than <int> distinct, valid alignments, bowtie2 does not gaurantee that the <int> alignments reported are the best possible in terms of alignment score. -k is mutually exclusive with -M and -a, and -M is the default.

Note: Bowtie 2 is not particularly designed with large -k in mind, and when aligning reads to long, repetitive genomes large -k can be very, very slow.
All the best
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Old 07-02-2012, 07:47 AM   #3
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Thanks dariober, that works! thanks a lot!
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align, bowtie, reads, sam bam, short read alignment

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