ChipPeak Analysis [How to plot colocalization of peaks around each other]

Question

[student12]

Hey Guyz, I have bed files associated with two different factors [Top2b and CTCF]. I have identified the peaks associated with each factor and the overlapping peaks using ChipPeak anno. I want to make similar plot as shown in the image, with top2b peaks distribution around CTCF peaks. Do U guyz have any suggestions. Your help is appreciated. Thank You.

PS: I have made overlapping plots around TSS, 5'UTR and 3'UTR using ChipeakAnno, but im having difficulty understanding how to plot averaged binding patterns of Topo 2b within a 4 kb window of all CTCF peaks.

Image Reference: Madabhushi R, Gao F, Pfenning AR, et al. Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. Cell. 2015;161(7):1592-1605. doi:10.1016/j.cell.2015.05.032

[Ram]

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

Answer 1

[guandongshang]

you can first use the computeMatrix in deeptools , then use matrix result to get this plot using plotProfile in deeptools.