Correlation Plot of Two Biological Replicates of GRO-seq Data

Question

[LDT]

Dear all,

I have a question regarding the data analysis of GRO-seq data. How do people create correlation plots between replicates?

Do they compare the number of read counts in each position, or are they using any other method. In a fundamental GROSeq paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522910/, they talk about this plot here.

but its not clear after reading it what they compare? RPKM values? BAM counts? any idea?