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  • cuffdiff output files are empty

    Hi,

    I downloaded the new version of cufflinks and tried to use cuffdiff. I just used the -N option for upper quartile normalization and my output files are empty. I got the following warning messages

    [09:52:55] Modeling fragment count overdispersion.
    Warning: fragment count variances between replicates are all zero, reverting to Poisson model
    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: 93.00
    > Read Type: 50bp single-end
    > Fragment Length Distribution: Truncated Gaussian (default)
    > Default Mean: 200
    > Default Std Dev: 80


    And this was repeated quite a number of times with different upper quartile values.

    Note: I am using the .gtf file downloaded from ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/ (for the hg18 build)

    Thank you

  • #2
    Could you post the command line that you use? Also the whole process should be started from cufflinks, then cuffmerge/cuffcompare, then at last to cuffdiff.

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