Alignment Of Tsms Data

Question

[kanwarjag]

I have a data generated from Helicos using tSMS technology. I tried Bowtie it did not turn out to be good. I was reading on web and turn out SHRIMp2 may be useful as reported by authors. I was wondering: 1. Any good aligner (SE) for human ref genome with data generated by Helicos 2. What will be the best parameters to use for SHRIMP2. I can use default but may have to tweak into few for tSMS type of data.

Thanks