Plot coverage per base for BAM file I have a BAM file and a BED file for my own chromosome. I would like to get coverage per base and _ideally_ construct a histogram of coverage across each gene. The motivation is to visualise the coverage across each gene. If my experiment is good, I should expect uniform coverage. It's also important to compare the coverage near the boundary of the genes. A R (bioconductor) solution is ideal, because I can directly visualise. How to do it?

From your bam-file, you can generate a BED(-graph) of per base coverage with bedtools genomecov (use the -ibam, -d and if you want a BEDgraph also the -bg flags).

There are multiple R packages for bioconductor which read and visualise these, including sushi.