In this study, for the first time, a comparison of single-relaxation-time, multi-relaxation-time and entropic lattice Boltzmann methods on non-uniform meshes is performed and application of these methods for simulation of two-dimensional cavity flows, channel flows and channel flows with sudden expansion is studied in the slip and near transition regimes. In this work, Taylor series expansion and least squares based lattice Boltzmann method is utilized in order to apply the lattice Boltzmann models on non-uniform meshes. A diffuse scattering boundary condition and a combination of bounce-back and specular boundary conditions are employed to obtain the slip at the walls. Besides, the relaxation times of lattice Boltzmann methods are computed in terms of Knudsen number. Different lattice Boltzmann methods are used to simulate lid-driven micro cavity flows and their results are compared with each other and with those obtained in the literature. Then, the best model in accuracy and stability, i.e. multi-relaxation-time lattice Boltzmann method, is applied to simulate the micro channel flow in different Knudsen numbers. Results show that the proposed method on non-uniform meshes is capable of simulating micro flows problems in the slip and the transition regimes.