How to make a TSS enrichment plot in ATAC-seq analysis, which shows the TSS enrichment of nucleosome-free fragments, mono-nucleosome fragments, and di-nucleosome fragments?

![enter image description here][1]


I see a tutorial (https://rockefelleruniversity.github.io/RU_ATAC_Workshop.html) about TSS enrichment plot, which uses `soGGi::plotRegion` function, I am wondering what is meaning of `score` in the plot? How should I normalize the score value based on the total reads?

![enter image description here][2]


  [1]: /media/images/01ecf3cd-a185-4ae5-bcbe-96b96d9e
  [2]: /media/images/386e3b84-2ef9-4c35-8c0f-8603af09

Thanks

Not sure what the Score is actually quantifying, but you can do a simple min-max normalization to force the score values to be between 0 and 1 (ie fraction of signal). This looks like a glorified wrapped of the `rtracklayer` and `GViz` packages. 

Truthfully, I found using the `Deeptools` suite really easy. Customization might be a little trickier, but it was super fast and the raw data is output so you can bring that into R and plot using `ggplot` if that's more your speed.