I am back again with one more naive question.
What according to you is the best way to normalize multiple BAM files to one another?
My goal is to simply normalize a set of BAM files, then plot the avg read coverage.
I've attached an example of a read metagene plot showing the avg read coverage with BAM files that are not normalized to one another. To reiterate, my goal is to normalize these BAM files, then make the same type of plot.