Cody's, located on Telegraph Avenue, near the UC Berkeley campus is a great alternative to bigger chain stores like Barnes 'N Noble or Border's. Cody's has competitive prices, and a huge selection of books. It's easy to get spend hours browsing through the selection, finding all kinds of gems. The staff is very helpful and friendly, and will help you locate any book you're trying to find. I've also found them to be pretty knowledgeable about literature. They also carry a huge assortment of magazines, so if you're looking for your favorite obscure publication, they just may have it.
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