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<div>Hi</div>
<div> Yes upgrading fixed my problem. Try running from the terminal using the fastq file, if that works it has to be a galaxy issue. </div>
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<div style="font-size:75%; color:#575757">Sent from Samsung Mobile</div>
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-------- Original message --------<br>
From: "Miskey, Csaba" <Csaba.Miskey@pei.de> <br>
Date: 06/09/2013 19:25 (GMT+07:00) <br>
To: bio-linux@nebclists.nerc.ac.uk <br>
Cc: tbooth@ceh.ac.uk,Jeremy Shearman <jeremy.she@biotec.or.th> <br>
Subject: Biolinux7_Galaxy_Tophat_error <br>
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<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">Dear Guys,</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">I wonder if Jeremy’s problem with Tophat (error when trying to run it) was solved by updating to 2.0.9.</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">My Galaxy running under Biolinux7 has Tophat 2.0.9. and I still cannot make it run. (Bowtie accepts and runs ok with the same fastqsanger file with which Tophat
throws the error. Though, as I figured the two mappers take the same set of indexes).</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">Any help would be greatly appreciated!</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">Best wishes,</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">Csaba</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">(new in the field)</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">Hi Jeremy,</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">I've pushed the update through for Tophat so it should become available</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">later today.</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">Note that bowtie is a legacy program that is unlikely to be updated</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">again. The latest bowtie2 is packaged separately in the bowtie2 package</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">(currently 2.1.0).</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">Cheers,</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">TIM</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">On Tue, 2013-08-27 at 06:44 +0100, Jeremy Shearman wrote:</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">> Hi Tim
</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">> Can you please update the bio-linux tophat version to</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">> v2.0.9 because the current bio-linux version (2.0.8) is not compatible</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">> with the current bio-linux version of bowtie (v1.0.0) and throws an</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">> error when you try and run tophat.</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">>
</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">> Thanks</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black">> Jeremy</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Arial","sans-serif"; color:black"> </span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Courier New"; color:black">Csaba Miskey Ph.D.
</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Courier New"; color:black"> </span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt; font-family:"Courier New"; color:black">Paul Ehrlich Institut
</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Courier New"; color:black">Medical Biotechnology</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt; font-family:"Courier New"; color:black">Paul Ehrich Str. 51-59</span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt; font-family:"Courier New"; color:black">63225 Langen, Germany</span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt; font-family:"Courier New"; color:black"> </span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt; font-family:"Courier New"; color:black">Tel: +49 06103 773407</span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt; font-family:"Courier New"; color:black">csaba.miskey@pei.de</span></p>
<p class="MsoNormal"><span lang="DE"> </span></p>
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