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Travel from Shinjuku to Nikko using a JR pass

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I want to use my JR pass to travel to Nikko. We will be staying in the Shinjuku area. When i check hyperdia for the scedule, it looks to me that the trains leave from Tokyo station. But when I checked the forum on japan guide, people have said that you can go to Nikko from Shinjuku. Do they mean take a regular train to Tokyo station and swithch to a Nikko bound train. Or is there a train bound for Nikko that leaves from Shinjuku station?

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