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Forum: Bioinformatics 02-15-2009, 09:36 AM
Replies: 236
Views: 586,996
Posted By myrna
Suboptimal hits

Novoalign will do this for you. You might have to play around with the parameters to get exactly what you want (how many suboptimal hits, how suboptimal etc).

Ryan
Forum: Bioinformatics 10-20-2008, 03:48 PM
Replies: 236
Views: 586,996
Posted By myrna
Bowtie

Hi Jerry.
How well (if at all) are indels handled by Bowtie? I have found Novoalign to handle gaps better than Maq and SOAP. By the way, I am looking forward to seeing the release of TopHat....
Forum: Bioinformatics 09-21-2008, 11:01 PM
Replies: 236
Views: 586,996
Posted By myrna
This seems pretty off-topic. From the...

This seems pretty off-topic. From the information on the DNAbaser website, it only handles capillary sequence data. Not at all what this forum is about.
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