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  • How does cuffdiff/cufflinks determine "read type"?

    From a recent cuffdiff run:
    Code:
    > Map Properties:
    >	Total Map Mass: 5798099.00
    >	Number of Multi-Reads: 0 (with 0 total hits)
    >	Read Type: 106bp x 106bp
    >	Fragment Length Distribution: Empirical (learned)
    >	              Estimated Mean: 171.87
    >	           Estimated Std Dev: 55.64
    > Map Properties:
    >	Total Map Mass: 5795202.00
    >	Number of Multi-Reads: 0 (with 0 total hits)
    >	Read Type: 105bp x 105bp
    >	Fragment Length Distribution: Empirical (learned)
    >	              Estimated Mean: 171.90
    >	           Estimated Std Dev: 55.69
    These are from 100bp x 100bp reads, why would cufflinks believe that they are 105bp or 106bp paired-end reads?

  • #2
    I have the same problem. I used cufflinks 1.0.3.

    Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
    > Map Properties:
    > Upper Quartile: 366.70
    > Read Type: 108bp x 102bp
    > Fragment Length Distribution: Truncated Gaussian (default)
    > Default Mean: 200
    > Default Std Dev: 80

    Comment


    • #3
      I cannot understand why there is this warning. I have trimed my data, is this the reason?

      Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.

      Comment


      • #4
        I also get the same warning. I am also using trimmed reads. Can any one explain why cufflinks thinks that the reads are single end even though the bam file was produced using paired reads in tophat?

        Comment

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