Tophat Multi-Thread

[ECHo]

Hi, I've used the following command:
./tophat -r 5 -p 12 ../bowtie-0.12.1/indexes/chr21 ../bowtie-0.12.1/TestData/s_1_1_sequence.txt ../bowtie-0.12.1/TestData/s_1_2_sequence.txt

-p 12 I think it could use up to 12 core/thread processing
So, I use "top" command to see the system monitor.
However, the bowtie operation, which is called by tophat uses only 100%CPU.
Why not approaching 1200%CPU usage?

Thanks.

[ECHo]

kind of weird...
now it shows 1200%CPU

Don't know why?

[Cole Trapnell]

This is normal - not all phases of the TopHat run are multi-threaded.