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  • babi2305
    Member
    • Feb 2013
    • 14
    #1

    How cuffdiff works?

    Greetings everyone!

    I am stuck with cuffdiff output. Can anyone please give me an idea about how cuffdiff works? I am more interested in finding novel genes/isoforms. I gave the combined.gtf (from cuffcompare) file & sam files of both my samples to cuffdiff as input. I want to know, which genes/isoforms are the one that are novel with respect to the other sample. Does cuffdiff returns the novel ones also or just the differently expressed known genes between two samples?

    I ran cufflinks with -g option to get the novel transcripts. Somebody please tell me how cuffdiff works?

    Thanks
    Tags: None
  • turnersd
    Senior Member
    • May 2011
    • 115
    #2
    Perhaps not the most accessible description, but this is from the official documentation:

    404 Not Found
    http://cufflinks.cbcb.umd.edu/howitworks.html#hdif

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