I have been trying to analyze a chip-seq sample from GEO and I don't understand the ouput of covplot function, I have full black bar on almost all chromosomes, is it the result of byproduct from the immunoprecipitation ? the bed file is also missing score values, could it be the problem ?
My second concern is that the chipset is targeting a protein that I found downregulated on all microarray with the same treatment and cell type. Is it possible to confirm that with ChipSeeker ? or should I re-run macs2 using the Control vs Treatment instead of Treatment vs Control to see If I get peaks at the location of the protein ?