I am performing ChIP-seq of histone modifications in S. cerevisiae. The trouble occurs when I am using MACS. If I use the correct genome size of 1.2e+7 and almost any value of MFOLD (as low as 3), I don't get any peaks. If the only parameter I change is the genome size to 2.7e+9, I get peaks, albeit they are not correct.
Since it is histone mods and not TF binding, is MACS even appropriate to use? Would SICER be a better choice?