tophat running parallel

[mirreke]

Hello,

I'm running tophat with -p 4 to run on four cores simultaneously.
It seems that bowtie runs on 4 cores indeed, but the whole process spends much more time on "segment_juncs" which runs on one core only.

Is there a way to run the segment_juncs part in parallel as well?

Kind regards,

Mirreke.

[mbblack]

Look in the documentation, but I'm pretty sure that bowtie is the only part of the package that is threaded. Everything else is going to be a single-cpu program.