Question: Effective Genome Size Of Mm10 For Macs14
1
gravatar for Sukhi Singh
8.4 years ago by
Sukhi Singh10k
Netherlands
Sukhi Singh10k wrote:

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 • 6.3k views
ADD COMMENTlink written 8.4 years ago by Sukhi Singh10k
2

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 REPLYlink written 8.4 years ago by matted7.4k

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

ADD REPLYlink written 8.4 years ago by Sukhi Singh10k

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 REPLYlink written 6.3 years ago by Madelaine Gogol5.2k
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