Scientists have traditionally applied algorithms developed for ChIP-seq, without an input DNA control, to detect enriched DHSs although peculiarities of DNase-seq data render this approach unsuitable without adjustment of default settings at minimal [128]. Currently, the most widely used peak-calling algorithms for DNase-seq data analysis are the publicly available F-Seq [129], Hotspot [130], ZINBA [131] and MACS [132–135] (Step 7). F-Seq and Hotspot represent the only tools specifically developed for handling the unique characteristics of DNase-seq data. ZINBA can be applied as a general peak-calling algorithm for many types of NGS data and MACS, although initially developed for the model-based analysis of ChIP-seq data, has been successfully used as a peak-caller for DNase-seq data in many instances [136]. All these tools are based on different algorithms, parameters and background evaluation metrics (for details read [135]).
