Finding All Possible Exact Matches With Bowtie

Question

[jensenkristian89]

Hello.

I am currently trying to match a large set of DNA sequences (~10,000 sequences, ~20 bp each) to the entire human pre-mRNA, looking only for exact matches. Most methods I've used have been far too slow, until I found Bowtie. After indexing the pre-mRNA (took a few hours) it can do the matching in a few minutes. However, it only finds ~60% of the possible matches, even with the -a flag. Is there a way to find all matches with Bowtie (possibly sacrificing some of its speed) or is incomplete sensitivity just a drawback of the algorithm that allows the impressive speed?

I have read the Bowtie paper, but unfortunately I don't quite understand every part of the algorithm.

Thanks!

[Matt LaFave]

What arguments are you using besides -a?

Answer 1

[Rm]

try using –v 0 -a OR since reads of 20bp reduce the seed length: -n 0 -l 20 -a

or try Blat ?

[jensenkristian89]

I've tried both, the result is the same.

[Rm]

same as what? to 60%?