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It depends on the FPGA.
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All Cyclone devices have a weak pull-up after power-on and during configuration. Value between 7k and 352k depending on IO voltage and PVT (Process, Voltage, Temperature). See page 457 (Volume 3 page 1-11 Table 1-12) of the Cyclone IV Handbook
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Some FPGAs have an IO_PULLUP pin that can be used to define whether weak pull-ups are enabled or not during power on, i.e., you have a "global" option, rather than a per pin option.
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I don't recall Cyclone devices to have this feature.
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Generally I use pull-up or pull-down resistors on control signals that I want to guarantee have a particular state when the FPGA is not configured.
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Usually you would only need external pull-down resistors, but they may have to be as low as 1k, external pull-up resistors can be any value.
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