<div dir="ltr"><div>Dear Suzanne,<br><br></div>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.<br><br>Cheers,<br><br>Steve<br><div class="gmail_extra"><br><div class="gmail_quote">On 30 January 2015 at 12:00, <span dir="ltr"><<a href="mailto:bio-linux-request@nebclists.nerc.ac.uk" target="_blank">bio-linux-request@nebclists.nerc.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Date: Thu, 29 Jan 2015 09:55:47 -0600<br>
From: Suzanne Gomes <<a href="mailto:suzanneluziagomes@gmail.com">suzanneluziagomes@gmail.com</a>><br>
To: <a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a><br>
Subject: [Bio-Linux] Tophat2 multithread<br>
Message-ID: <<a href="mailto:E5BB2F1E-3DDF-4879-A5F7-A333C2F8B7D2@gmail.com">E5BB2F1E-3DDF-4879-A5F7-A333C2F8B7D2@gmail.com</a>><br>
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<br>
Hi,<br>
<br>
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?<br>
<br>
Thanks<br>
<br>
Suzanne
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