Is it really required to do GC normalization ATAC seq data ?
One of the paper where they have ATAC seq data did the normaisation of GC bias after peak calling. When i looked for the library and the reason why GC bias i found this
Could it be true that genes with higher GC content are higher expressed? It has been suggested that genes that are either extremely high or extremely low expressed are under some form of selection leading to “extreme” GC content. What CQN does, is making the effect of GC content comparable across samples, and we show in  that this leads to improved inference. It also flattens the effect of GC content on gene expression, but we believe this is better than having the effect of GC content depend on the sample. https://www.bioconductor.org/packages/release/bioc/vignettes/cqn/inst/doc/cqn.pdf
Now that scenario is for RNA seq would it be logical to do the same for ATAC seq?