Number of nucleosomes identified in treatment and control with varying binding and support regions. (A) The scatter plot shows all combinations of nucleosome predictions in treatment and control obtained for the chosen range of parameter values. Points corresponding to maximum number of predicted nucleosomes in the treatment sample for a given number of predicted nucleosomes in the control are marked in green. Results from parameter sets where b = 147 are highlighted in red. Solid points indicate parameter combinations that were selected for further analysis. (B) Log ratio of the number of nucleosomes identified in treatment and control for each combination of binding and support region length. Parameter combinations corresponding to green points on the left are marked with ×. Green symbols indicate parameter combinations chosen for further analysis.