I am having a problem running Cuffdiff on some RNA-seq data.  I want to
compare 2 of my conditions.  I successfully used Cuffdiff three days ago to
compare two sets of data that are processed the exact same way (align with
Tophat and use Picard to confirm adequate alignment). I am using Galaxy
through MAIN and I tried Cuffdiff with these samples on 1/18 and 1/19.
Here's the error:

An error occurred running this job: *cuffdiff v1.3.0 (3022)
cuffdiff --no-update-check -q -p 8 -c 1000 --FDR 0.050000 -b
/galaxy/data/hg19/sam_index/hg19.fa --labels DMSO,E2

Thanks for the help.
Erin Shanle

Graduate Research Assistant
Molecular and Environmental Toxicology
425 McArdle Laboratory for Cancer Research
1400 University Ave
Madison, WI 53706
608 262 9834
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