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.cuffli...@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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