Thank you very much Jeremy.<div><br></div><div>Can I have a look at the re-ran datasets?</div><div><br><br><div class="gmail_quote">On Thu, Oct 13, 2011 at 12:12 PM, Jeremy Goecks <span dir="ltr">&lt;<a href="mailto:jeremy.goecks@emory.edu">jeremy.goecks@emory.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word">Chandu,<div><br></div><div>There are two problems:</div><div><br></div><div>(1) you mapped your reads to AgamP3, but the dbkeys for all of your Cufflinks datasets is anoGam1. This should not have happened automatically with Galaxy, but I&#39;m looking into the issue now. Did you do this yourself?</div>
<div><br></div><div>(2) Galaxy does not have sequence data for anoGam1, and this directly led to the problem that you&#39;re seeing.</div><div><br></div><div>I corrected the problem by manually assigning build AgamP3 to your Cufflinks datasets and then rerunning Cuffcompare. In the future, I expect that we&#39;ll add anoGam1 data to our public server, but it&#39;s not clear when this will occur.</div>
<div><br></div><div>Thanks,</div><div>J.</div><div><div></div><div class="h5"><div><br></div><div><br></div><div><br><div><div><div>On Oct 12, 2011, at 5:35 PM, Chandu Galaxy wrote:</div><br><blockquote type="cite">Thank you Jeremy. I&#39;ve shared my History named &#39;Mosquito Work: RNA-Seq analysis 2&#39; with you just now. Please see the datasets from 1-58 (also see deleted datasets). Thanks.<div>
<br></div><div>--</div><div>Chandu<br>
<br><div class="gmail_quote">On Wed, Oct 12, 2011 at 2:02 PM, Jeremy Goecks <span dir="ltr">&lt;<a href="mailto:jeremy.goecks@emory.edu" target="_blank">jeremy.goecks@emory.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

<div style="word-wrap:break-word">Chandu,<div><br></div><div>Are you running your analysis on our public server ( <a href="http://main.g2.bx.psu.edu/" target="_blank">main.g2.bx.psu.edu</a> )? If so, can you share your history me please (Options--&gt;Share/Publish--&gt;Share with a User--&gt;my email address).</div>

<div><br></div><div>Thanks,</div><div>J.</div><div><div></div><div><div><br><div><div>On Oct 11, 2011, at 4:26 PM, Chandu Galaxy wrote:</div><br><blockquote type="cite">Thank you for the response.<div>I can&#39;t check my reference genome dataset because I&#39;m using reference provided by Galaxy (<b>Mosquito (Anopheles gambiae): AgamP3</b>). Is there any solution? Thank you.</div>

<div><br>
</div><div>--</div><div>Chandu</div><div><br></div><div><br></div><div><br><div class="gmail_quote">On Mon, Oct 10, 2011 at 7:15 AM, Jeremy Goecks <span dir="ltr">&lt;<a href="mailto:jeremy.goecks@emory.edu" target="_blank">jeremy.goecks@emory.edu</a>&gt;</span> wrote:<br>


<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><div><br><blockquote type="cite"><span style="border-collapse:separate;font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><span style="color:rgb(48, 48, 48);font-family:&#39;Lucida Grande&#39;, verdana, arial, helvetica, sans-serif;font-size:12px;line-height:14px;background-color:rgb(255, 255, 255)">Tool execution generated the following error message:<pre style="font-family:monospace;line-height:10px;background-color:white;color:black;border-top-style:dotted;border-right-style:dotted;border-bottom-style:dotted;border-left-style:dotted;border-top-color:black;border-right-color:black;border-bottom-color:black;border-left-color:black;border-top-width:1px;border-right-width:1px;border-bottom-width:1px;border-left-width:1px;overflow-x:auto;overflow-y:auto;padding-top:10px;padding-right:10px;padding-bottom:10px;padding-left:10px">
Error running cuffcompare. Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to benefit from the most recent features and bug fixes (<a href="http://cufflinks.cbcb.umd.edu/" target="_blank">http://cufflinks.cbcb.umd.edu</a>).
No fasta index found for ./input1. Rebuilding, please wait..
Error: sequence lines in a FASTA record must have the same length!
</pre></span></span></blockquote></div>Chandu,</div><div><br></div><div>Cufflinks/compare/diff requires that your reference genome dataset have the following format:</div><div><br></div><div>&gt;my_chrom</div><div>AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT</div>


<div>AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT</div><div>AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT</div><div>...</div><div><br></div><div>Note that all lines of sequence data have the same length. </div>


<div><br></div><div>The problem you&#39;re seeing is because there are lines in your sequence data that are not the same length, e.g.</div><div><br></div><div><div>&gt;my_chrom</div><div>AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT</div>


<div>AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTA</div><div>AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCG</div><div>...</div></div><br><div>The FASTA Width tool in Galaxy can help you format your dataset correctly.</div>


<div><br></div><div>Good luck,</div><div>J.</div></div></blockquote></div><br></div>
</blockquote></div><br></div></div></div></div></blockquote></div><br></div>
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