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  • RNASeq

    Dear,
    anyone could help me to "understand" the outputs of cufflinks?
    How can I use these data and FPKM values to extract the differential gene expression and the different abundance of isoforms?

    Moreover, where can I find a gtf annotation file for human to integrate in the run of cufflinks as -g parameter?

    thanks a lot
    ME

  • #2
    Hi,

    There's a verbose description of each column under http://cufflinks.cbcb.umd.edu/manual...uffcomp_output

    Also, in my experience, for a lot of technical questions and concerns the FAQ is helpful, http://cufflinks.cbcb.umd.edu/faq.html

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