comprehensive TF motif databases generated using in vivo/in vitro assays or computationally based de novo motif discovery algorithms. More importantly there is an imminent need to further investigate the applicability of DNase-seq, and ATAC-seq for that matter, to accurately detect factor-chromatin interactions in dynamic cellular settings. It is possible that future footprinting algorithms will be able to accurately identify only a subset of TF binding events based solely on analysis of footprints with high depth (above a statistically validated threshold), and not on generic analysis of all cleavage profiles.
