So lets hope that you guys sort of understand what I'm attempting to do.
I am looking at three histone marks. H3K4me1 is one of these marks and it is used in many studies to identify probable enhancer regions.
I've noticed that when looking in IGV, I see some really nice enhancer regions that seem to have a reoccuring pattern, but I can't seem to find a way to identify these 'regions'.
I am trying to find H3K4me1 regions that have flanking peaks and a middle section of low signal. Similar to this: /\__/\
My question is: Is there a way to identify these regions using a already developed tool? Maybe something like bedtools? Or bedops? Essentially I am looking for regions of H3K4me1 where Pol can bind inbetween H3K4me1 peaks.
This is a good example of what I'm talking about (the region distal from the tss):
Any ideas? Or would something like this require some advanced scripting/coding and thus be unfeasible for a wet lab research assistant?