Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq.

A common objective across ATAC-seq and ChIP-seq analyses is to identify differential signals across contrasted conditions. However, in differential analyses, the impact of copy number variation is often overlooked. Here, we demonstrated copy number differences among samples could drive, if not dominate, differential signals. To address this, we propose a pipeline featuring copy number normalization. By comparing the averaged signal per gene copy, it effectively segregates differential signals driven by copy number from other factors. Further applying it to Down syndrome unveiled distinct dosage-dependent and -independent changes on chromosome 21. Thus, we recommend copy number normalization as a general approach.