Metrolink can take you to Oceanside. And if the schedule meets, you can take Coaster train from Oceanside to San Diego. There's also the Sprinter light rail at Oceanside you can take to Escondido. If you want a direct train ride to San Diego, go to the Fullerton Station and hop on the Amtrak.
The Orange County Line, which is the 600 series Line, takes you as far out as Oceanside.
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