Hello 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 /galaxy/main_pool/pool2/files/003/607/dataset_3607369.dat /galaxy/main_pool/pool2/files/003/590/dataset_3590726.dat,/g* 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 sha...@wisc.edu
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