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The PCIe hard IP core is natively Avalon-ST. To get the Avalon-MM interface a soft Avalon-ST to Avalon-MM bridge has to be added, and you can only get that if you instantiate the core in Qsys. If you don't use Qsys you only get to use the native Avalon-ST version.
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Got it. I was talking with a colleague yesterday about this issue and he also suggested trying to instantiate it in Qsys. I was able to do that in the latest Quartus Prime (17.0). This is my first time using Altera tools, so I am still getting used to everything.
Thank you for your explanation as to why it can only be instantiated in Qsys. That makes more sense.
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