I want to know how the profiles of the RNAPII is over the genes in which a peak of a specific gene (also a ChIP seq experiment) has been called, in different conditons to know whether these genes are differentially transcribed because of the condition and that's why my gene is recruited there. To do so I selected the TSS in the annotation of my gene of interest (after annotation with ChIPseeker). Once I have the specific TSS of my gene, I've used this list to generate my computeMatrix using deepTools (in spite of the complete tss file ffrom USCS), and could see the profiles of the different condition over the specific TSS of my gene of interest. I'm not sure if this approach is right or I miss somthing, I appreciate so much if someone could give me any feedback!!