Hello, I have 3 Atac-seq samples which I have normalized across them using MAnorm2 algorithm. (https://github.com/tushiqi/MAnorm2). What I obtained are the different peak regions and the corresponding normalized read counts. I have a list of gene locations of my interest
However, for representation, I wish to use deepTools to plot profile or heatmap for the gene locations of my interest. For this I have to use the computeMatrix which in turn requires bigwigs. How can I go about this? Any alternative method to normalize the bam files of the 3 samples ?