bamCompare can be used to generate a bigWig or bedGraph file based on two BAM files that are compared to each other while being simultaneously normalized for sequencing depth.
If you are not familiar with BAM, bedGraph and bigWig formats, you can read up on that in our ../help_glossary
Warning
The filtering by deepTools is done after the scaling factors are calculated!
Warning
If you know that your files will be strongly affected by the kind of filtering you would like to apply (e.g., removal of duplicates with --ignoreDuplicates or ignoring reads of low quality) then consider removing those reads beforehand.