Stratified pipe flow in a pipe has been the subject of several investigations over the years. In fact it is relevant to the operation of thermal energy systems involving significant temperature gradients and low flow conditions. Stratification affects mixing, and is one the key phenomena that need to be addressed in the design of any mixing system of devices involving significant density difference. In order for thermal stratification in a pipe to be correctly modeled the underlying hydrodynamic behavior related to the mixing of two streams in a pipe needs to be fully understood. The present paper deals with the numerical simulation of the flow in a pipe where the bottom half has a lower velocity compared to the upper half. A turbulent mixing layer develops in the streamwise direction at the interface between low flow region and higher flow region. Since the Reynolds number is low, the boundary layer and the mixing layer are about the same size. This translates in non trivial interactions between the structures in the boundary layer and the mixing layer. The failure of RANS models in accounting for the mixing points in this direction. An LES of the flow in this geometry has been performed with the spectral code Nek5000. The averaged statistics have been compared with available experimental results. Proper Orthogonal Decomposition has been applied to clarify outstanding issues in RANS modeling.