cuffdiff with more than 2 conditions and replicates

[meono]

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:

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