Table 2.

Comparisons between ChIP-seq and ATAC-seq

Factor	ChIP-seq	ATAC-seq
Dependence on antibody	Yes, ChIP-seq requires good and specific antibodies	No
Throughput for detection	Only for Specific proteins	Global chromatin accessibility
Controls	Required, for distinguishing real peak regions from artifacts	Usually not required, but naked DNA controls are useful for characterizing the sequence bias of enzymatically induced cleavage
Results	Direct interactions between proteins and DNA	Potential binding sites for regulators