RSeQC provided bedfile does not work with read_distribution.py
Ok, I figured it out already, it's and old issue I come accross every now and then. The original bed file lists the chromosomes as chr1,chr2,...,chrX whereas my bam files uses 1,2,...,X

I fixed the bed file like this (python3):

import pandas as pd
bedFile = '/hg38_Gencode_V28.bed'
bedFile = pd.read_csv(bedFile, sep='\t', header=None)
bedFile[0] = [value.strip('chr') for value in bedFile[0]]
newBedFile = 'hg38_Gencode_V28_reformatted.bed'
bedFile.to_csv(newBedFile, sep='\t', header=None, index=None)


And now read_distribution.py works.