Read density heat maps were created by first using HOMER to generate read densities and then visualized using Java TreeView (http://jtreeview.sourceforge.net). To define the overlapping of two ChIP-seq, for instance of OLIG2 and H3K9me3, we first found out OLIG2 binding peak centers, then checked out H3K9me3 enrichment around these peak centers by using ComputeMatrix. And then visualized using PlotHeatmap. Motif analysis was carried out with HOMER.
