Hello,<div><br></div><div><br></div><div>I&#39;m using Galaxy tool from about two months. I&#39;m very new to this community. I ran into some problems when using the tools for NGS: RNA Analysis. I would like to get from the community. Here is the description of the problem.</div>
<div><br></div><div><span class="Apple-style-span">I&#39;ve four different datasets (</span><span class="Apple-style-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(204, 255, 204); ">fastqsanger format</span><span class="Apple-style-span">). I ran the </span>NGS: RNA Analysis tools like &quot;Tophat for Illumina&quot;, &quot;Cufflinks&quot;, &quot;Cuffcompare&quot;. The Tophat and cufflinks tools are working fine but the cuffcompare is giveing out an error message like the below.</div>
<div><br></div><div><span class="Apple-style-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); "><h2 style="color: rgb(2, 56, 88); margin-top: 0px; ">
Dataset generation errors</h2><p><b>Dataset 57: Cuffcompare on data 20, data 23, and others: combined transcripts</b></p>Tool execution generated the following error message:<pre style="font-family: monospace; line-height: 10px; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; 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; background-position: initial initial; background-repeat: initial initial; ">
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">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>The tool produced the following additional output:<pre style="font-family: monospace; line-height: 10px; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; 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; background-position: initial initial; background-repeat: initial initial; ">
cuffcompare v1.0.3 (2403)
cuffcompare -o cc_output  -s  ./input1 ./input2 ./input3 ./input4</pre></span></div><div><br></div><div>Can anyone help me to figure out what the problem is? Let me know if you need more information. Thank you.</div><div>
<br></div><div><br></div><div><br></div><div>--</div><div>Chandrasekhar</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div>