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What are you talking about? On-chíp termination (not reasonable with unused signals, I think) or weak pull-up resistors? The latter can be globally enabled for all unused pins which is the default setting with newer chips.
Cyclone III has only limited OCT capabilities by the way. So you should better clarify, what you mean.
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What I meant was that since I'm using the pins for on-chip termination, i.e. they are not receiving or sending signals, do I still have to define them in my top entity or just set them to OCT capabilities in the assignment editor?
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