I have bam/bedgraph files of read enrichment across the genome from ChIP-seq and DNase-seq biological replicates. I also have bed files of called peak regions of these samples as well.
I'm trying to figure out the best way to graphically compare the replicates by plotting them on two different axes to see if there the data looks similar across the genome.
I am thinking of graphing them in R but I am not sure if there is already a package in R/Bioconductor that does this or another tool and I do not yet know how to treat genome coordinates in R.
Any advice or suggestions would be greatly appreciated. Thanks