I was wondering if there is good way to draw coverage plot from bed file? My bed files are only contain chrome, start, end and its states, look like this:
chr1 958551 958621 state2 chr1 958681 958751 state2 chr1 961931 962011 state2 ...
Now I would like to see the state distribution from 20k upstream from TSS to 10k downstream from TTS (include gene body). I was trying to use plotProfile function in deeptools but the result is always a straight line, I guess it is because the input I give is:
chr1 958551 958621 2 chr1 958681 958751 2 chr1 961931 962011 2 ..
But I really don't have score for the bed file. Thanks for any suggestions!