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You need to convert your .sof into a .jic, and then use the programmer to flash it into the EPCS chip. Have a look at an370 (
http://www.altera.com/literature/an/an370.pdf) for more details.
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Thanks Daixiwen I think this concludes that I cannot achieve what I was hoping as I am using a 3rd party JTAG system on our production line and required JAM files - hoping to put the SFL in the FPGA followed by the final JAM image in to the AS device.
I think I will have to go back to the JTAG supplier and work out why it didn't work with my JAM file created from the JIC i.e. with the SFL integrated. :confused: