I have two different ATAC-seq libraries that I wish to compare on a genome browser. I have used Macs to generate bedgraph files for each individual library using the command:
macs2 callpeak -t macs2 callpeak -t bamfile --outdir /path/to/ -f BAMPE --keep-dup all --pvalue 1e-2 --call-summits --bdg
I then convert bdg to bigwig.
How can I best normalise the two ATAC-seq libraries that I want to compare by library size? Can I do this in MACS? Or do I do it after I have generated the separate bdg files?