Dear all,

Perhaps a simple question but one I have not been able to find a consensus on. I have two biological replicates of active PolII (PolII Ser5) CHIP-seq data plus an INPUT replicate. I am trying to generate a single fold enrichment (or log2 ratio or similar) value for PolII per gene in my yeast genome to visualise as a heatmap.

My current thoughts are to use deeptools BAMcompare or similar to generate log2 ratios across the genome then bedtools intersect (or map?) to give a single value per gene. Another idea would be to call broad peaks using MACS2 and intersect the gene and peak bed files. A third idea would be to generate RPKM values per gene from the PolII raw counts.

Are any of these approaches sensible? Ideas on better approaches would be appreciated. Thanks!