Entering edit mode
10.9 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
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...
Yeah, I think the results wouldn't be effected that much, still just thought someone have already done the exercise calculating it :)
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