I'm trying to plot the counts of the overlap of the regions of 1 bed file on the regions of another bed file (the second file has same width regions in different parts of the genome) in a histogram like plot in base pair resolution. But what ever I have tried (using bedtools/bedops - binning,counting and windows- e.g. this suggestion for motifs Which tool can plot the enrichment of specified motif across ChIP-seq bed files? ) doesn't seem to give me something informative. Is there an easy work around the problem? Thanks in advance
UPDATE: still not what I am looking for given in the answers!
Trying to explain it again: 2 bed files trying to get the counts of overlaps of one bed file to the other's file regions. Then plot the count frequency of overlaps (not sure if i should call that density) in a base-pair resolution on y-axis and bases (e.g. 0-300) depicting the regions from the second bed file on x-axis.