<p><i>Bin size</i>: Size (in bp) in which the genome was fragmented to analyze the histone mark distribution. <i>Differential score</i>: value generated by chromstaR which provide an estimation on how divergent two bins are (0 = no difference, 1 = extremely different). <i>Minimum read count</i>: 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. <i>False discovery rate</i> = minimum value to eliminate false positives. <i>Gap</i> = 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 <i>S</i>. <i>mansoni</i> genome. The reason for that is only uniquely mapped reads are used, but 47.73% of the genome is repetitive [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1007066#ppat.1007066.ref036" target="_blank">36</a>].</p
