I am in the process of comparing the similarity between two ChIP-seq conditions. According to the Deeptools documents, multibamsummary computes the read coverages for genomic regions for typically two or more BAM files whereas multibigwigsummary computes the average scores for each of the files in every genomic region.
I am having difficulty understanding the difference between the two tools and which one I should use. What is the difference between read coverage and average scores? Does the scale of the average score change depending on sequencing depth? Could someone shed some light on this please? Thank you in advance.