# All scripts run in Ubuntu 14.04 and Red Hat Enterprise Linux Server 7.3	
script_1.pl	Generates bigwig files for ratios from sorted bed files. Requires bedGraphToBigWig from ucsc. (Fig. 3A)
script_2.pl	Calculates min, max, mean and median lengths of peaks. (Fig. 3B)
script_3a.pl	Identifies unique genes from bedtools intersect output of peaks and gene bed file. (Fig. 3D)
script_3b.pl	Calculates genes per mb for unique genes in peaks. (Fig. 3D)
script_4a.pl	Calculates ratios for samples in PML regions. (Fig. 4B)
script_4b.pl	Calculates ratios for samples in random regions the size of PML regions. Requires bedtools. (Fig. 4B)
