For FAIRE-seq data the algorithm MACS [132] has been further extended to MACS2 (https://github.com/taoliu/MACS/) and performs reliably in identifying genomic regions of open chromatin (Step 10). This application is invoked by using the command macs2 callpeak and can be combined with the options broad, broad cutoff, no model, no lambda (unless a control file is given) and shift size. The algorithm uses default peak calling (q = 0.05) and broad (q = 0.10) cutoff values, but these settings can be adjusted or converted to P-values empirically. Once the peak-calling cutoff is set as a P-value, the broad cutoff value is automatically perceived as P also. The shift size parameter should be set as the midpoint of the average sonication fragment length in the analyzed dataset. In addition, upon availability a matched control sample can be used as input to increase detection confidence. In this case, command line parameters should be adjusted accordingly. FAIRE enrichment can also be detected using ZINBA [131]. As mentioned above, this software improves detection accuracy when the signal-to-noise ratio is low or in complex datasets. However, for high signal-to-noise datasets it performs equally well with MACS, although it is much more computationally intensive.
