While the Clipper Card system was down, each transit agency appeared to independently make the same decision to continue running without charging riders.

The San Francisco Bay Ferry raised its commuters’ costs by 3%. Drivers on the Golden Gate Bridge will also see costs increase by 50 cents, going to $9.75 for FasTrak users and up to $10.75 for those who get a toll invoice .

The Clipper card system used by transit agencies throughout the Bay Area remains down Tuesday due to a computer outage. Veronica Macias reports.