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


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



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