I want to plot the coverage across a region of a chromosome from a .bam file. I thought this was pretty straight forward, but for some reason I am not getting the correct coverage using bedtools coverage.
Here is what the .bam-file looks like in IGV:
Notice that there are almost no reads mapping to the introns.
And when I calculate the coverage using:
coverageBed -d -b SRR_1.420.bam -a features.bed > SRR_420.cov
I get this (NB the x-axis coordinates are wrong):
Any Idea what is happening? Link to the input files