I am currently planning to do ChIP-seq and have therefore been mapping some available data from ENCODE to gain some experience.
Common programs such as MACS can accomodate two input files i.e. sample and control. How does one deal with e.g. 1 treated sample and 1 un-treated (control) sample both for which an input control is also available?
Is it best to use the input control for each sample, and then make comparisons between peak calls following the actual peak calling? Or are the treated and non-treated samples normalized to their respective input controls prior to peak calling using normalized treated and non-treated inputs in e.g. MACS?
Common programs such as MACS can accomodate two input files i.e. sample and control. How does one deal with e.g. 1 treated sample and 1 un-treated (control) sample both for which an input control is also available?
Is it best to use the input control for each sample, and then make comparisons between peak calls following the actual peak calling? Or are the treated and non-treated samples normalized to their respective input controls prior to peak calling using normalized treated and non-treated inputs in e.g. MACS?