to use multi-core in Tophat

[IrisZhu]

Does anyone know how to use parallel computing in Tophat?

The option "-p" is not working for me -- my command is:
"tophat -p 10 -r 100 hg19 mate1.fa mate2.fa" but there's still only one CPU processing.

Any idea?

Thanks a lot,

Iris

[Thomas Doktor]

TopHat does some steps along the way which are not parallellized, you probably monitored TopHat's CPU usage during one of those steps. Try monitoring TopHat during the alignment steps and see if it isn't using several threads.