mismatch

[kylle345]

Hi,

I am currently working with 36bp reads from the solexa platform. I want to find a program (or specific settings) that will allow up to 5 mismatches.

Any suggestions?

Thanks

[nilshomer]

Hi,

I am currently working with 36bp reads from the solexa platform. I want to find a program (or specific settings) that will allow up to 5 mismatches.

Any suggestions?

Thanks

A number of aligners can be tuned for sensitivity, including BFAST, MAQ, Bowtie etc. I am the author of BFAST, so PM if you need help with adjusting sensitivity with BFAST. Threads for other aligners can also be found in the forums (with their respectful authors).