I need help regarding analysis of data that I obtained after ChIP with antibodies for different histone modifications. So, I have couple of chromatins, all from the same cell line, but with different treatments. I did ChIP with H3 antibody and with antibodies for different H3 modifications. I have some differences, but I was wondering how to analyze them. Obviously, I can't use some other region as negative control since all regions have H3. So, does anybody have experience with this? I don't know whether some differences that I see in the raw data are due to different starting amounts of chromatin or are real differences (changes in the chromatin structure after the treatment etc). is it OK just to analyze data versus input and flag (that is my negative control antibody)?