DRA829J: How to generate PCIe Reset?

Stephen, 

Sorry for the delayed response. 

I assume you are referring to the functionality of the PERST signal as it appears on standard PCIe slots, where the host can issue a reset (Fundamental Reset as defined in PCIe spec.), to the end-point that is plugged into the slot. 

If so, then yes this is done through a GPIO pin, where you can select a GPIO pin from DRA829, assert the pin as reset signal. The EVM uses a I2C GPIO expander, but this is to accommodate large set of pins used by the EVM for different systems. In actual user board, you can use a GPIO. Additionally, you can modify the dts file to tell Linux driver which GPIO is used, then the driver will toggle the pin for PCIe reset. 

Please also note that PCIe can issue in-band Hot Reset also. But it sounds not what you wanted.

please let me know if further clarifications are needed. 

Jian