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  • cuffdiff replicates empty results

    I use cuffdiff to detect differential expressed genes in two samples, since each has 2 replicates, so i use commas to separate replicates.

    Code:
    cuffdiff -m 40 genes.gtf  /60PO/accepted_hits.bam , /6124/accepted_hits.bam /3584/accepted_hits.bam , /4189/accepted_hits.bam
    It gives empty results;

    But if I run:

    Code:
    cuffdiff -m 40 genes.gtf  /60PO/accepted_hits.bam /3584/accepted_hits.bam
    It works fine.

    I have no idea why the replicates doesn't work.

  • #2
    Unfortunately, I can't provide you a solution, I'm interested in the answer, I also have a problem with the replicates, but I don't get empty resuts (http://seqanswers.com/forums/showthread.php?t=13868). The only difference is that I didn't use the option -m. Did you try without?

    Comment


    • #3
      A version of the following seems to have worked for me:
      Code:
      cuffdiff mm9_ensembl.combined.gtf -N -u -p 8 -L Label1,Label2 -b ~/bowtie/indexes/mm9.fa -o Label1_vs_Label2_ensembl L1/L1_accepted_hits.bam,L4/L4_accepted_hits.bam L2/L2_accepted_hits.bam,L3/L3_accepted_hits.bam
      It looks like you've added a space in your comma separated list. I wonder if that's the cause of your problem (I've not looked through the code for cuffdiff to see how it reads in its arguments, but it's not uncommon to take a space as a separator between positional arguments).

      Comment


      • #4
        Sorry, where did I add a space in my list? I don't see differences between our commands, except the options:

        Code:
        cuffdiff -L Raman,HM1 -N --FDR 0.05 /path/fichier.gtf /path/Cufflinks/L2/accepted_hits.bam,/path/Cufflinks/L4/accepted_hits.bam,/path/Cufflinks/L6/accepted_hits.bam /path/Cufflinks/L3/accepted_hits.bam,/path/Cufflinks/L7/accepted_hits.bam,/path/Cufflinks/L8/accepted_hits.bam

        Originally posted by dpryan View Post
        A version of the following seems to have worked for me:
        Code:
        cuffdiff mm9_ensembl.combined.gtf -N -u -p 8 -L Label1,Label2 -b ~/bowtie/indexes/mm9.fa -o Label1_vs_Label2_ensembl L1/L1_accepted_hits.bam,L4/L4_accepted_hits.bam L2/L2_accepted_hits.bam,L3/L3_accepted_hits.bam
        It looks like you've added a space in your comma separated list. I wonder if that's the cause of your problem (I've not looked through the code for cuffdiff to see how it reads in its arguments, but it's not uncommon to take a space as a separator between positional arguments).

        Comment


        • #5
          It's in the initial post ("/60PO/accepted_hits.bam , /6124/accepted_hits.bam" has two spaces in it surrounding the comma), not the one you just placed. Perhaps it's just a artifact of the forum software, then.

          Comment


          • #6
            Ok, I see...
            Which version of Cuffdiff do you use?
            I'm using the version 0.9.3 and I just read that the version 1.0.0 allows to handle the replicates. This could explain the problem...

            Comment


            • #7
              Ah, that'll probably do it then. I'm using the most recent (1.0.3).

              Comment


              • #8
                I confirm, the version was the problem ! So to handle replicates, the version 1.0.0 at least is necessary

                Comment

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