Yes, but each device has a different configuration method.

Cyclone IV GX devices can be connected to x2 devices by selecting x2 when generating the PCI-Express core.

In Stratix V GX, Stratix IV GX, and Arria II GX devices, you can select x4 when generating the PCI-Express core and link to x2 with auto-negotiation when connected.

For details, search for the keyword "PCI Express Hard IP Configurations for the PCI Express Compiler" in the user guide at the URL link below and refer to it.
  https://www.altera.com/en_US/pdfs/literature/ug/ug_pci_express.pdf