can someone help me understand the differences between bedtools' genomecov and deepTools' bamCoverage? Are they used interchangeably, are there key differences, can I generate the same results with both tools? I have sequencing data from a paired-end PRO-seq experiment and for generating the coverage tracks I am not sure which tool to "trust", as I have not been able to reproduce their respective results with each other.
Any experience, thoughts, directions? I am grateful for any input!