genomic configurations [56]. A number of methods have been applied to measure nucleosome positioning [48, 58, 111, 144] and occupancy [48, 145] from MNase-seq data based on the number of sequence reads that start at each base pair, assessed for a consensus nucleosome position or in a per base pair basis [56]. In addition high-resolution MNase-seq data generated using a modified paired-end library construction protocol can be analyzed using V-plots to detect TF binding. V-plots are two dimensional dot-plots that display each fragment’s length in the Y-axis versus the corresponding fragment midpoint position in the X-axis [50].
