Effective Genome Size Of Mm10 For Macs14

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13.0 years ago

Sukhi Singh 11k

Has anyone already figured out the effective or mappable genome size of mm10 to be used with Macs as an input argument.

-g GSIZE, --gsize=GSIZE Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs

Thanks

macs chip-seq • 10k views

ADD COMMENT • link updated 3.7 years ago by Ram 45k • written 13.0 years ago by Sukhi Singh 11k

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Any reason you don't want to use the mm9 value? I can't imagine it's that different, and if their method is that sensitive to this parameter, you probably won't be too happy anyways...

ADD REPLY • link 13.0 years ago by matted 7.8k

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Yeah, I think the results wouldn't be effected that much, still just thought someone have already done the exercise calculating it :)

ADD REPLY • link 13.0 years ago by Sukhi Singh 11k

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I'm going to try this tool GEM for a different genome, you could try it. https://groups.google.com/forum/#!topic/macs-announcement/-iIDkVwenn8

ADD REPLY • link updated 3.7 years ago by Ram 45k • written 10.9 years ago by Madelaine Gogol 5.3k

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