Differential input pair LVDS for the ADC5272 in Cyclon 3

Answering your questions:

1. is it possible to use the I/O pins as the LVDS differential inpus?

- I believe you are referring to using single ended IO pin as differential input. Ideally you could do that by inverting the input signal to one of the input pin to make up p and n pair. However, you should expect skew between the p and n legs since you have a inversion in place. The dedicated LVDS input is design to ensure minimal skew between p and n legs.

2. can i use some channels from Clock part?

- Generally the dedicated clock input pins will have dedicated routing to clock network. Not sure if Quartus II will allow you to use as normal input. You could did a quick try by running Quartus II compilation.