Hello, I'm analyzing some ChIP-seq data (bam files) through deepTools' bamCoverage and bamCompare. I'm new to biological data analysis and I don't understand the difference between scaling (option --scaleFactorsMethod in bamCompare) and normalizing (option --normalizeUsing).
BamCompare doesn't allow the usage of both (scaling the 2 compared bam files and individually normalizing the bam files).
My questions are:
What do they mean with scaling? When should I use it?
What do they mean with normalization? When should I use it?
Which one accounts for sequencing depth?