[Bio-Linux] Tophat2 multithread

[Steve Moss]

Dear Suzanne,

Use the -p flag to tophat to increase the number of threads (see all flag
options using tophat --help), e.g. tophat -p 24 for 24 threads. Note that
not all stages of the pipeline are parallelised, however.

Cheers,

Steve

On 30 January 2015 at 12:00, <bio-linux-request at nebclists.nerc.ac.uk> wrote:

> Date: Thu, 29 Jan 2015 09:55:47 -0600
> From: Suzanne Gomes <suzanneluziagomes at gmail.com>
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: [Bio-Linux] Tophat2 multithread
> Message-ID: <E5BB2F1E-3DDF-4879-A5F7-A333C2F8B7D2 at gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi,
>
> So I have Tophat2 running, but each run is taking at least 7 hours (not
> sure how long exactly as I?ve been leaving it overnight). Just wondering
> how I would go about increasing the number of threads Tophat2 uses in order
> to reduce the run time?
>
> Thanks
>
> Suzanne




-- 

Steve Moss
about.me/gawbul
[image: Steve Moss on about.me]
  <http://about.me/gawbul>
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