Due to a problem in the Quartus® Prime version 16.0 software, you will see no transceiver links when you open TTK on a PCIe® interface. See this screenshot .
This is due to missing clock connections for the PCIe module's Transceiver Reconfiguration Controller.
To work around this issue, edit the instantiation <your design name>_altera_pcie_a10_hip_* of the Hard IP for PCI Express module and add the PCIe reference clock to the Transceiver Reconfiguration Controller connections as shown below. Replace <refclk_clk> below with the actual PCIe refclk signal used in your design.
FROM:
.xcvr_reconfig_clk (1'b0),
...
.reconfig_pll0_clk (1'b0),
...
.reconfig_pll1_clk (1'b0),
TO:
.xcvr_reconfig_clk (<refclk_clk>),
...
.reconfig_pll0_clk (<refclk_clk>),
...
.reconfig_pll1_clk (<refclk_clk>),
This problem is scheduled to be fixed in a future version of the Quartus Prime software.