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Old 03-10-2014, 08:46 AM   #1
Location: Milwaukee

Join Date: Dec 2011
Posts: 72
Default Cuffdiff thread option

Can anyone explain to me the following option in CuffDiff:

-p/--num-threads <int>
Use this many threads to align reads. The default is 1.

What are threads? Will it take longer to run the analysis if multiple threads are used? Will such an analysis be more accurate?
gwilymh is offline   Reply With Quote
Old 03-10-2014, 09:44 PM   #2
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Location: UK

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These are the individual processes that are used by cuffdiff. For example if you have a hyper-threaded core-i3, use -p 4. It uses as much CPU power as possible. So it shortens the analysis time. If you have a 4-core CPU, you are better off using -p 8. It depends on how many thread your processor can handle.
urostor is offline   Reply With Quote

cuffdiff, cufflinks, thread

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