Using EPCQ to load Nios

Thanks for your reply. I don't want to use Quartus II Programmer because

a) I don't want the whole chip to be erased each time I program,

b) I want the NIOS Cpu to be able to program the EPCQ flash itself, and so the nios2-flash-programmer has to work.

I'm using a Cyclone V 5CSTFD5D5 part.

I have read an736, thank you. Is there any particular part you wanted to refer to?

I think the pertinent point was from Cris72, when he said the EPCS pins need to be configured as general purpose I/O - but Quartus 15.1 doesn't let me do that.