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  • cuffdiff with more than 2 conditions and replicates

    Hi,

    I am sure this is trivial to most but I couldn't figure it out myself. I am trying to get cuffdiff to work on 3 conditions and 3 replicates. As far as I can figure out, I am supposed to pass the path for the bam/sam files through a text file. What I don't know if how to pass this file to cuffdiff on command line. I expected it to be something like this:

    Code:
    cuffdiff -o diff_out -b genome.fa -p 8 -L C1,C2,C3 -u merged.gtf inputFileList.txt
    where inputFileList.txt would have the paths to replicates on the same line separated by commas and conditions C1-3 on separate lines.

    Well, this didn't work for me and when i tried to enter the paths on the command line, I would only get comparison for C1 and C2. The rest of the combinations are missing.

    I would appreciate some help here, if you've done this before or know how to.

    Thanks

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