In a typical MNase-seq experiment, chromatin accessibility is probed indirectly by deciphering areas of the genome that are occluded by nucleosomes (Figure 1). The location of each mapped tag is identified by the genomic coordinate of the 5′ end in the forward or reverse strand and represents the strand-corresponding nucleosome border (unshifted tag) [125]. Tags can also be shifted 73 bp [111] or extended for 120 to 147 bp [48, 113] towards the 3′ direction to represent the midpoint or full nucleosome length respectively. For organisms with short linkers a 120 bp extension provides better nucleosome resolution and reduces overlaps between neighboring nucleosomes [113]. With paired-end sequencing, the nucleosome midpoint is assumed to coincide with the midpoint of the forward and reverse reads. To map consensus nucleosome positions representative of the average cell population, overlapping reads have to be clustered over genomic regions (Step 5).
