Thanks to the Sloan Digital Sky Survey, we now know that the Universe becomes opaque to Ly$\alpha$ photons at $z \sim 6$. This presents an obvious challenge for attempts to study the Universe at high redshifts with quasar absorption lines. I discuss two ways to extract more information about reionisation than the simple presence of complete Gunn-Peterson absorption. First, we still expect to see metal line absorption red-ward of Ly$\alpha$. This will allow us to probe the early phases of metal enrichment in the intergalactic medium; the lines can be quite strong because the enriched regions are relatively compact. This is particularly important because metals are a crucial feedback mechanism in the early Universe. Second, we expect to see isolated Ly$\alpha$ transmission features even before the final stages of reionisation. These features allow us to learn about the topology of reionisation and the condensation of the cosmic web at $z \sim 6$.