I need some suggestions on how to associate a score to nearest gene from peak score. I have elongating form of Pol2, and almost all the peaks (using macs2) are contained inside gene-body. I use bedtools intersect to annotate the peaks to genes. However, I am not sure how to proceed to transfer this score on to genes.
We want to find the transcription rate from the peaks which in our data will always be within the gene-body due Ser2-5 phosphorylation, should I still use the distance to peak center to calculate the gene-wise score? It will also be helpful if you can direct me to any protocol papers.