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There are three ways to get across the Bay.

Service Cost Notes
AC Transit Transbay Service $4.20/one-way or $151.20/month fastest option if you live near a bus stop; drops off at Transbay Terminal, then connect to office via bike share at station. 36 rides or 18 commute round-trips makes the monthly pass worthwhile
Bikes on BART varies bikes allowed all hours, but crowded during peak hours; swinging through Oakland stations makes this slower than AC Transit Transbay Service
MacArthur Bike Shuttle $1 cheapest option, if full take BART
SF Bay Ferry $4.75 on ClipperCard connects Jack London Square and SF Ferry Building; can take bike onboard

If you connect by bicycle, you have these options to avoid having to take the bike onto the train:

Service Cost Notes
Berkeley Bike Station Free valet and self service, no overnight parking
BikeLink Parking 5¢/hour bike to station, lock bike, then take BART
Bay Area Bike Share $88/year last mile between BART/Transbay Terminal and office
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