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Old 10-19-2011, 04:06 PM   #1
lewewoo
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Default Tophat help: how to maximize CPU performance

We have got a huge amount of RNAseq data and we would like to optimize/maximize the performance of our computer (wisely use the computer resources to speed up assembly step).
Any suggestions for this?
I know there is -p/num-threads for Tophat, how to use it and what is your suggestion for our CPU and memory?
2 X 2.93 GHz 6-Core Intel Xeon
24GB 1333MHz DDR3
Thanks a lot!
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Old 10-19-2011, 04:16 PM   #2
lewewoo
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some people said 1 thread per core, so I should set up -p 6? Thanks!
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Old 10-19-2011, 05:23 PM   #3
frozenlyse
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Don't you have 2x6 cores so 12 cores in total? Anyway a lot of the steps in TopHat aren't multithreaded so you definitely won't get a linear speedup with more threads.
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Old 10-19-2011, 06:09 PM   #4
lewewoo
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Thanks!
Yeah, 12 cores, so can set up 12 threads; and the data set is too big and really need cut off the time of assembly; btw, which steps do you know are multipl-treaded? i saw some people said Bowtie and other people said adjunction parts?
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