I am about to do ChIP-Seq analysis allele specific way. I have not done ChiP-Seq analysis practically, but I have some idea about how to do it. The problem is I'm not getting any answers for doing ChIP Seq allele specific way. I have done allele specific RNA Seq analysis. I have the two parental genomes as well. From what I have read so far, after aligning the ChIP-Seq, we do peak calling and it gives us a bed file. So
Is it same as RNA-Seq? Should I align the ChIP reads to both the parental genomes?
After peak calling, should I intersect the bed file to my vcf file like in RNA-Seq or there is another way of doing ChIP-seq allele specfic way?
Or it is not possible altogether and I'm barking the wrong tree?