Hello<br>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&#39;s the error:<br>
<br>An error occurred running this job: <i>cuffdiff v1.3.0 (3022)<br>cuffdiff
 --no-update-check -q -p 8 -c 1000 --FDR 0.050000 -b 
/galaxy/data/hg19/sam_index/hg19.fa --labels DMSO,E2 
/galaxy/main_pool/pool2/files/003/607/dataset_3607369.dat 
/galaxy/main_pool/pool2/files/003/590/dataset_3590726.dat,/g</i><br clear="all"><br>Thanks for the help.<br>-- <br>Erin Shanle<br><br>Graduate Research Assistant<br>Molecular and Environmental Toxicology<br>425 McArdle Laboratory for Cancer Research<br>
1400 University Ave <br>Madison, WI 53706<br>608 262 9834<br><a href="mailto:shanle@wisc.edu">shanle@wisc.edu</a><br>