Regarding the metagene package (http://www.bioconductor.org/packages/release/bioc/html/metagene.html).
I am using paired-end bam files as input. The plots which I generate with metagene look reasonable, but I am wondering what exactly is plotted. Does metagene consider the first base of each mate, or the middle of the insert?
Basically I am wondering which base(s) are used for producing the plot when using paired-end bam files, and whether one pair leads to one or two "counts" contributing to the underlying matrix.