The sensitivity and specificity of ATAC-seq is similar to DNase-seq data obtained from approximately three to five orders of magnitude more cells, and it diminishes only for really small numbers of cells [103]. The ATAC-seq protocol does not involve any size-selection steps and can thus identify accessible locations and nucleosome positioning simultaneously. However, its ability to map nucleosomes genome-wide is limited to regions in close proximity to accessible sites [103]. The most challenging aspect of ATAC-seq is the analysis of the sequence data, since generalized methods are unavailable or limited. With the additional demonstrated ability for analyzing a patient’s epigenome on a clinical timescale [103], we foresee ATAC-seq to become the preferred method for the study of chromatin structure in the near future.
