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Bowtie behavior in latest releases

Posted by dawe on 11 Aug 2009 at 15:15 GMT

As Bowtie and SeqMap do not map reads with more than three mismatches between the read and the reference sequence, reads spanning exon-intron boundaries have frequently more than three mismatches and are therefore not mapped.

Since release 0.10.1 bowtie allows a seed length shorter than 20 bp (down to 5 bp). In principle this means one can allow for 3 mismatches in 5 bp. I haven't tested yet, but it may be a workaround for mismatch limitations.

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