Using BFast with Short SOLiD Reads

[AmitL]

Hi,

In BFast documentation it says:
"We assume your reads are at least 50bp in length."

How can I use it for shorter reads? 35 bases or so.

Cheers,
Amit

[nilshomer]

Try the "bfast+bwa" branch. Where are you getting the 35bp data from (is it fragment data)? Typically we only see 35bp data when it goes along with a 50bp paired end read.

[AmitL]

That's right. It's paired end data.

I'll try the "bfast+bwa".

Thanks.

[Chipper]

I have used the normal BFAST version with 35bp and 50 + 35 bp with reasonable results, except for some pairing issues that I think have been solved in the current version.