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Altera_Forum
Honored Contributor
16 years agoleen's description of the IDE answers your second question.
The other problem (in your second paragraph) has to do with the device that you are programming. In JTAG mode, you are programming the Cyclone II, so that should be the device in your device chain, and your programming file would be an sof file. In Active Serial mode, you are programming a non-volatile chip (like an EPS serial chip), and that chip must be "seen" by the programmer (you may have a PROG switch on your board, for example). You would need a corresponding pof file, built for that chip.