Stable binding of TFs in the vicinity of DHSs protects DNA from nuclease cleavage and generates DNase I footprints that at high-sequencing depth can unveil occupancy of TFs with long DNA residence times (for example CTCF and Rap1) [84, 85]. Thus, high-coverage DNase-seq data can be analyzed with specialized algorithms to detect long-standing TF binding (Step 8). Previously specialized algorithms developed for DGF have identified hundreds of TF binding sites at genome-wide resolution, by comparing the depth of DNase I digestion at TF binding sites to adjacent open chromatin and taking into account only raw counts of 5′ ends of sequencing tags [19, 78, 83, 128, 146–149]. However, some of these algorithms are inefficient for mammalian genomes [130] or publicly unavailable. The latest publicly available footprinting algorithm, DNase2TF, allows fast evaluation of TF occupancy in large genomes with better or comparable detection accuracy to previous algorithms [85]. However, it still suffers from detection inaccuracies stemming from transient TF DNA residence time and the inherent cutting preferences of DNase I like all currently available footprinting algorithms [85].
