Parameters used in chromstaR for the detection of ‘ranges’ (10 kb to 100 kb).

Bin size: Size (in bp) in which the genome was fragmented to analyze the histone mark distribution. Differential score: value generated by chromstaR which provide an estimation on how divergent two bins are (0 = no difference, 1 = extremely different). Minimum read count: minimum number of reads which must be mapped inside a bin in order to take it into consideration. Minimum region length: minimum size (in bp) of consecutive adjacent bins with a different chromatin profile between samples. False discovery rate = minimum value to eliminate false positives. Gap = size of gaps which are allowed between two bins or group of bins with a different chromatin profile between samples. This is important, as gaps (where no reads are present) are frequent on S. mansoni genome. The reason for that is only uniquely mapped reads are used, but 47.73% of the genome is repetitive [36].