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-p or number of threads in Tophat2

Hi,

Whats meaning of -P or --num-threads in Tophat 2 ? For Tophat running , how can i set up it? My question is whats the meaning of 1 or 2 or 8 in this option?

Thanks

rna-seq
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updated by Devon Ryan Devon Ryan • written by Arash • Arash

1 answer

It's (roughly) the number of cores on your computer that it can use in parallel. If you don't know how many you have, then ask whoever the systems administrator is.

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written by Devon Ryan Devon Ryan

Thanks:

Intel® Xeon(R) CPU E5-2620 v4 @ 2.10GHz × 32 Memo: 62.8 GiB

so, whats the number for -p ?

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written by Arash • Arash

Nothing over 12 according to the specs.

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written by Devon Ryan Devon Ryan

@Arash: You don't want to use 12 if this is a single CPU machine. Depending on how the program is written it may lock the machine up if it starts using all 12 cores. You should leave a couple of cores for system programs to do their thing so you are able to interact with the system (i.e. use the keyboard and have the system pay attention to it).

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written by GenoMax GenoMax

@genomax2 : Whats your recommendation?

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written by Arash • Arash

If you are the only user on this machine then use 8 or 10. A couple cores more or less will not reduce/increase the run time by a significant amount.

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written by GenoMax GenoMax

Even for interactive machines, leaving a half core for browsing the internet usually suffices.

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written by Devon Ryan Devon Ryan

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