I have been trying to generate a gene coverage plot from my bam file using Gene Body Coverage (BAM) from Galaxy.org, but keep getting results that I am not expecting (see the attached heatmap png). While the png file suggested all samples have a shart peak near the 40th percentile, it is very different from what I see when I visualise my data on IGV. So I am wondering if my input bed12 file is in the wrong format.
I have attached a screenshot of my bed12 file (see the screenshot png below). Would you mind checking if the bed12 file is in the right format?