In this talk, I explain the search for tau neutrino appearance in the atmospheric neutrino flux at Super-Kamiokande with a particular emphasis on the effect deep inelastic cross section uncertainties have on interpreting the result. In particular, I explain why the normalization of the DIS cross-section also needs to be treated as a parameter in the fit of tau normalization, and show how a neural net based on event parameters can separate various cross-section modes in the background sample. © 2011 American Institute of Physics.