I am attempting to re-create a heatmap found in this article (Figure 3 B, the MNase-seq one). They rank genes / TSS by length of the nucleosome free regions surrounding the TSS.
I would like to do something similar using DNase-seq data. I have created many heatmaps before, but I am not typically sorting genes / TSS this way. Sorting by length of -1 nuclesome to the +1 nucleosome.
How would I go about creating a heatmap like this? How do I apply my DNase-seq data to find these regions, and then rank them by their length?