I am attempting to re-create this figure from this link http://figshare.com/articles/_Enrichment_of_RNA_polII_on_the_exon_sides_of_exon_intron_and_intron_exon_junctions_/372514 (Figure A and B, the junction figures). I currently use a combination of ngsplot and deepTools for most of my metagene plots, but I have no idea how I would be able to plot something like this.

Any ideas?
I have not done something like that, but using deepTools this may work (assuming you have bigwigs for the sense and antisense):

1. get a a list of exon genomic positions, be sure that they contain the orientation.
2. For a figure similar to A, use computeMatrix reference-point, select as reference point the end of the region and 150 bp before and 150bp after the reference point.
3. For a figure similar to B do the same, except that you choose as reference point the start of the region.