Alpharettta will be the better commute though will still take 45 minutes on a good day and could be much longer on a bad one anywhere from 60 to 90 minutes. Personally I would consider a home closer in such as dekalb or gwinnett counties.
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Driving to Emory from Woodstock everyday should take only 45 minutes as well, but those 45 minutes are only available between the hours of 830pm and 530am.
If you work at night, that's OK. Otherwise, choose the GA400 corridor commute.
Regardless, commuting is an atrocious, life sucking option for too many Atlantans - what are the compelling reasons for commuting for hours everyday vs. choosing a Dekalb neighborhood?