As title, I am curious about how to do normalization between two Chip-seq data. When we are doing quantification analysis between two Chip-seq data, how can we know that the differences between two samples are due to the different condition?
Why I have this question is that I am currently reading a paper
"Epigenetic Regulation of Learning and Memory by Drosophila EHMT/G9a "
The article mentioned that "To compensate for differences in sequencing depth and mapping efficiency among the two ChIP-seq samples, the total number of unique tags of each sample was uniformly equalized relative to the sample with the lowest number of tags (7,043,913 tags), allowing for quantitative comparisons." I just don't get the point here that how the normalization is done.