I am attempting to create a metagene plot of Pol II on the center of exons. I am using deepTools to do this. I have a bed file with my region (exon) information, and a bigwig (and bam) file of Pol II scores. DeepTools has two modes ... reference-point, and scaled ... I am unsure of which to use and why. I am currently using reference-point center as that is what I am looking for, but I am aware that exons are of different lengths so they must be normalized.
What parameters should I should and why exactly?
PS: In the heatmaps generated, I am not entirely sure what the colorbars represent. Is it how strong the signal of a tf is?