We evaluate the prompt atmospheric neutrino flux including nuclear correction and $B$ hadron contribution in the different frameworks: NLO perturbative QCD and dipole models. The nuclear effect is larger in the prompt neutrino flux than in the total charm production cross section, and it reduces the fluxes by $10% - 30%$ depending on the model. We also investigate the uncertainty using the QCD scales allowed by the charm cross section data from RHIC and LHC experiments.
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