I have some Single end and Paired end ChIP-seq and ATAC-seq data. I have done aligning using Bowtie2 and ignored duplicated reads using Picard, then performed peak calling on Bam file using MACS2 (I just need peaks and I will not continue with Differential analysis).
I would like to normalize data based on sequence depth and I found I can do it using bamCoverage based on bam file and using cqn packages based on number of reads for each peaks. I prefer to do on bam file using bamCoverage but its out put is bigwig/bedgraph that is not suitable for peak calling by MACS2.
I would like to know is there any solution for that?