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Hi,
if I understood you right your core has to do some Lane Reversal?! This is not supported in the PCI Express MegaCore Functions. You can take a look in the attached erata sheet. Maybe this helps you out.
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The device EP2GX125DF35C5NES have a 3 GXB modules. Each GXB module have 4 lanes (4 rx and 4 rx). The KIT
http://www.altera.com/products/devkits/altera/kit-aiigx-pcie.html use GXB0 and GXB1 for PCIE. The GXB0 for PCIe 1x and 4x. GXB0 and GXB1 for PCIe 8x.
We made a board with EP2GX45DF29C5N. It have a 2 GXB modules. GXB0 and GXB1. We are connect GXB0 to four fiber optics transceivers. (it's worked good) and GXB1 to PCIe 4x. (it's did't worked at all (4x or 1x)). We don't use line reversal, polarity reversal etc. We have only one different. We are connect PCIe core to GXB1 module. Not to GXB0 as Altera kit.