Hello Alessia, This appears to be a known bug in Cuffcompare that can be worked around by reordering the input files: http://seqanswers.com/forums/showthread.php?t=5809 If you have questions about this, it would probably be worth asking the tool authors for input/advice at tophat.cufflinks@gmail.com. Best wishes for your project, Jen Galaxy team On 11/7/11 5:50 PM, Alessia D wrote:

Hi,

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:

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 (http://cufflinks.cbcb.umd.edu). Error: no XLocus created for transcript CUFF.34072.1 (file ./input3) [2, 2], on chrY+:274296-277218

However, if I run Cuffcompare on the 2 conditions separately (3x Cufflinks datasets), everything works fine. Does anyone know why this is?

Thanks

Alessia

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