I have done ChIP-Seq analysis alllele specific way somehow, I think. I aligned the ChIP-Seq data to both the parental genomes and then I merged the aligned BAM files and I did peak calling on the merged BAM file using MACS2. I got a BED file and a bedgraph file from it. I intersected that bedgraph file with the individual parental VCF files and got allele specific bedgraph files that converted to bigwig and I visualized in the IGV. Now I want to quantify those data and plot density plots of the TSS of the genes allele specific wise. After reading many papers and blogs and biostars, I got few words like spanning, windows, variable step and deeptools and what not. I know how to use deeptools but I don't think its giving results as I want. So can anyone make me explain step by step as how to do it. Any help is appreciated.
Thanks in advance.