I am currently newer to the computational biology field, however am very familiar with the biology aspect of genome wide experiments. Currently, I am attempting to call peaks using MACS1.4 on aligned BAM files. I noticed that in the control section of the peak calling, people tend to use Input as a control. I was wondering if someone could explain why this is used. To my logic, MACS uses the control it is given to calculate regions of binding enriched in the treatment file over the control, however if the input is given as the control, technically there really shouldn't be ANY regions where the treatment file is more enriched than the control, given that the treatment is an IP and the input contains all genomic DNA. Anyway, if someone could clear this up for me I would be grateful!