Bottom and charm productions has been measured separately in Au$+$Au collisions at mid rapidity and Cu$+$Au collisions at forward rapidity at $\sqrt{s_{NN}}$ = 200 GeV using the PHENIX silicon tracking system. In Au$+$Au collisions, we measured single electrons from bottom and charm hadron decays separately and found that bottoms are less suppressed than charms at 3 < $p_T$ < 4 GeV/c. In Cu$+$Au collisions, we measured $J/\psi$ from $B$ meson decay and found that the $B$ meson production at low $p_T$ is consistent with number of binary collision scaling at forward rapidity.