Read phasogram and peak histograms calculating process. A. Schematic description of the 1-pile read phasogram calculation. Blue arcs represent recorded distances between reads that map on the same strand. Not all distances are represented for better graphical visualization B. Schematic description of the 2-pile read phasogram calculation. Only distances between reads with at least 1 co-located read are taken into account. All distances taken into account are noted with blue arcs C. Schematic description of the peak histogram calculation. Paired end reads are coupled into fragments which are further trimmed by 40 b.p. around dyads so they all have length of 80 b.p. For the histogram calculation distances between trimmed fragments are recorded.