Hi, <div><br></div><div>I am trying to run Cuffcompare on a set of 6 Cufflinks-generated datasets (3 replicates of 2 conditions).  I am consistently getting the following error:</div><div><br></div><div><pre style="line-height: 10px; background-image: initial; background-attachment: initial; background-origin: initial; background-clip: initial; background-color: rgb(255, 255, 255); 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">http://cufflinks.cbcb.umd.edu</a>).
Error: no XLocus created for transcript CUFF.34072.1 (file ./input3) [2, 2], on chrY+:274296-277218
</pre></div><div><br></div><div>However, if I run Cuffcompare on the 2 conditions separately (3x Cufflinks datasets), everything works fine.  </div><div>Does anyone know why this is?</div><div><br></div><div>Thanks</div>
<div><br></div><div>Alessia</div><div><br></div><div><br></div>