We report about our methodology developed for the determination of the thermal capture cross section of various target isotopes at our PGAA and NIPS facilities, which both use a guided cold neutron beam produced by the 10 MW Budapest Research Reactor. The two facilities provide an excellent means for determining partial gamma ray cross sections for products produced in the sample by neutron capture reactions. Both stations are equipped with HPGe detectors to detect the gamma rays coming from the excited nuclei of the samples. We present examples for the determination of thermal capture cross section of various target isotopes including the radioactive 99Tc, 129I nuclei and of the 204,206,207Pb isotopes. The chopped beam option provides a good opportunity to study short-lived products.