I wanted to calculate IDR (irreproducible discovery rate) between two ChIP-seq samples to determine significant peaks (with IDR < 1%). Came across this R package 'IDR', but, as explained here, first would have to make sure IDR can be applied, i.e. Np/Nt < 2 and N1/N2 < 2. Is there any tool that can calculate Np/Nt and N1/N2? Which tools do you ususally use to determine IDR?