Bowtie2 in the Tophat/Cufflinks pipeline?

[jdanderson]

Hey Everyone,

Has anyone tried to plug Bowtie2 output into Cufflinks with success?

It seems as though Tophat may not be able to run on top of Bowtie2, is that accurate? If so, has anyone heard of plans for Tophat to be made compatible with Bowtie2 in the future?

Cheers,
Johnathon

[Nicolas]

It doesn't look like a great idea. I am not sure if the outputs of Bowtie and Bowtie2 are compatible. I asked the Bowtie2's developers if they had plans to integrate it in Tophat, but I didn't get any answer.
By the way, Cufflinks doesn't rely on an alignment algorithm. If Bowtie2 should be integrated, it should be in Tophat. That would be pretty cool.