The tool is at:
I want to get base coverage for specific regions (I'll provide a bed file). However, the output is not in a standard BedGraph format that I can export into R for visualisation.
Q: How do I draw density plot of coverage over the regions from the outputs generated by the coverage tool?
Q: Alternatively, how to convert the non-standard outputs to a proper BedGraph? For example, the Sushi R package takes a bedgraph input file.