Hi Yan,

Would you please submit this as a bug report? It helps if you leave all inputs undeleted in your history. Instructions:

http://wiki.g2.bx.psu.edu/Support#Reporting_tool_errors

Thanks!

Jen Galaxy team

On 8/16/12 6:18 AM, Yan He wrote:

Hello,

I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 samples (A and B). I did Cufflinks and Cuffmerge before running Cuffdiff. I ran Cuffdiff with the following options: Cuffmerge + Bowtie A, B (sorted required by Cufflinks after mapped with Bowtie). But I got the following error message:

*An error occurred running this job: /cuffdiff v1.3.0 (3022) cuffdiff --no-update-check -q -p 8 -c 10 --FDR 0.050000 /galaxy/main_pool/pool4/files/004/800/dataset_4800173.dat /galaxy/main_pool/pool3/files/004/799/dataset_4799827.dat /galaxy/main_pool/pool4/files/004/799/dataset_4799831.dat/*

*//*

Where did I do wrong? Thanks very much for your help!

Yan

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