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  • Method for calculating significant mutated genes of cancer study

    Dear everyone,
    For cancer study, significant mutated genes were calculated to predict driver genes. I also calculaed it for one project, but got few genes.
    MutsigCV brought few genes, as TP53.
    Oncodrive was performed, the same result as mutsigCV.
    Method as described of Kan depend on background mutation rate, also give few genes.

    In the three method, genes with p-value below 0.05 is more, and q-value <0.1 is less.

    MuSiC need many files, I haven't done it. Is there any other method? What's your processing with SMG?
    Are there any suggestions? Thank you!

  • #2
    FWIW, there are reasonably good instructions for installing MuSiC here:




    There are a ton of relevant questions on biostar that will aid you in getting the appropriate files together. We also monitor BioStar for keywords related to our software packages and will be happy to assist if you run into problems. Best of luck

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