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mutSigCV "category discovery" in coverage files

nzhaonzhao Seattle, WAMember

Dear MutSig Expert,

Could someone explain to me what exactly the "category discovery" does when running mutSigCV? This is the step when you input a common coverage file (such as exome_full192.coverage.txt) and select genome build as hg19 or hg18.

I get confused because I thought that by using exome_full192.coverage.txt, the coverage file should be the same across different analysis, which is not what I observed in real data analysis. I analyzed the LUSC data as in the example file and my own data set, mutSig gives different coverage files, although they both starts with file exome_full192.coverage.txt.

Any explanation is welcome. Thanks a lot.

Ni

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