Input control versus IgG¶

IgG controls and input controls in ChIP are two very different types of controls and cannot be used interchangeably in most projects. Input controls are where you sonicate chromatin and directly turn that into a library so it accounts for openness of the chromatin. This is the kind of control that MACS can correct for directly in its model. IgG controls are pull-downs with IgG agarose beads without any antibodies. These libraries tend to be sequenced at much lower depth than all other samples, are typically super sparse, typically break all QC metrics due to over PCR-amplification, and in many cases are not overall useful.