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.
See cgat bam2geneprofile --help for ways in which profiles can be normalised.
I've also found that removing overlapping genes can make a big difference to metagene profiles. I don't know if anyone has a better way to do this, but I do it using a combination of cgat and bedtools with: