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  • plefebvre
    Member
    • Jan 2010
    • 10
    #1

    Cufflinks then Cuffdiff

    Hi there
    I have ran a RNA-seq on Illumina GII, and processed the bam files on the Galaxy server. Everything ran smoothly untill I tried to run Cuffdiff on may assembled transcript files which always yields an error as this

    566: Cuffdiff on data 492, data 493, and data 521: CDS diff
    An error occurred running this job: cuffdiff v0.9.3 (1649)
    cuffdiff -q -p 8 -Q 0 -c 1000 --FDR 0.050000 -N -r /galaxy/data/mm9/sam_index/mm9.fa /galaxy/main_database/files/002/338/dataset_2338625.dat /galaxy/main_database/files/002/337/dataset_2337232.dat /galaxy/main_database/files/002/337

    Has somebody ever ran into this kind of problem (the Glaxy team sais this is a Cufflinks problem, but no answers yet from those guys ...)
    Thanks
    Tags: None
  • honey
    Senior Member
    • Feb 2010
    • 151
    #2
    error in Cuffdiff

    It appear that you are running on Galaxy you may like to post your question on their mailing list and may be there is some glitch in Galaxy

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