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  • Cuffdiff missing genes/transcripts?

    So i completed a tophat-cufflinks-cuffcompare-cuffdiff workflow using the cuffcompare combined.gtf file as the reference in cuffdiff. My assumption was that the number of genes and transcripts in the the final cuffdiff files e.g. gene_exp.diff should be the same as in the input Cuffcompare.combined.gtf.

    The input Cuffcompare.combined.gtf has 15126 distinct gene_ids while the cuffdiff output file gene_exp.diff has only 9029.

    So 6027 genes are "missing"

    The "missing genes are all single exon and are either class_code "." OR class_code "u" however not all genes of these classes are found in the "missing" list.

    Does any one know if there is a known reason why not all genes would be present in the cuffdiff output files?
    Last edited by swarbre; 05-30-2011, 11:21 PM.

  • #2
    Any ideas????

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    • #3
      Hello,

      Did you found answer !!
      Krishna

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      • #4
        I am having the same problem. I have one (single exon, class code u) gene missing from my Cuffdiff output that is present in my gtf file, which I made with Cufflinks and Cuffmerge. I also have >100 transcripts (but not their corresponding genes) missing from the Cuffdiff output.

        Did anyone find an answer?

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        • #5
          I would adjust adjusting the False Discovery Rate a bit, but more importantly increase the maximum number of fragments allows more gene Ids to be found. I believe the default is 1 Million.

          I had to play around with this Maximum Number of Fragments value to something like 10 to 50 Million to get the genes that I was interested to appear.

          I hope this helps a bit.

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