No. Comma isn't needed in this question at all. By the way, is this the question you meant to ask: Have n't you finished your paper yet?
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AnonymousBy the way, is this the question you meant to ask:Haven't you finished your paper yet?Not necessarily. Both "Haven't" and "Have" are correct in the question. "Haven't" implies the expectation that the paper is already finished, while "Have" communicates an expectation for it to not be done yet.