Transmutation reactions are the reactions in which there is a change in the nucleus of atom.
In Rutherford scattering experiment, nitrogen nuclei are bombarded with the alpha particles which results in the production of an oxygen nuclei, whereas in gold scattering experiment, the alpha particles only change their path while interacting with the gold foil. So, the basic difference between two experiments is their is change in the nuclei of atom in rutherford's experiment whereas there is not any type of change in nuclei in scattering experiment.
To make the transmutation reactions which involve gold nuclei and alpha particles, bismuth nuclei can be used as it is easier to get gold from bismuth.