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Yes that is possible. See this document:
https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/hb/cyclone-iv/cyiv-51008.pdf See figure 8 - 29. Also you will need to program using a .jic file. Use convert programming to create a jic file from your sof and hex (elf) files.
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My hardware setup is according to Fig 8-28. When I try to upload *.sof file using JTAG interface I get the error "Unable to read device chain", while programming of *.pof files is successful in AS mode using a separate header as in Fig 8-28.
I am wondering if there is an issue of device support, as the user manual of USB BLASTER II (Rev C) indicates support for Cyclone IV devices while the user manual of USB BLASTER Rev A does not.
https://www.altera.com/literature/ug/ug_usb_blstr.pdf https://www.altera.com/en_us/pdfs/.../ug/ug_usb_blstr_ii_cable.pdf
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