One important field of study is which and how histones are modified, and how this is related to cell types, expression of genes, and also to diseases. But how can these parts of the genome, where histones are modified, be found?
In principle, a sample of similar cells is collected and tested. First, we want to know, where at the genome are the histones. This forms our basis called background. Second, we want to know if the histones found are modified. This forms the test called experiment. Both together form a data set. What we get after analyzing and some (in fact quite complex) preprocessing, is an annotated genome, where we have a sequence of nucleotides and the information whether this sequence is associated with a histone (background) and if this histone is modified (experiment). However, the latter information is not directly encoded in the data. It has to be extracted from the data by a peak-caller.