Hi I guess this is a sort of naive question. In some papers, there are some Venn diagrams showing the overlap of TFs/Histone modifications bound peaks. I was wondering how they get the overlap. I checked the methods, but could not get the information, maybe this is too rudimentary that people even do not bother to write it down in the method part.
Now I have a ChIP seq data for a DNA binding protein, and H3K27ac, and want to see to what extent they overlap with each other. To that end, I called the peaks by "macs2", with the option "--broadPeak", and tried to get the overlapped regions by:
bedtools intersect -a proteinA_cellX_peaks.broadPeaks -b H3K27ac_cellX_peaks.broadPeaks
Then I could get a long list of something like:
chr7 127471196 127472363 Pos1 0 + 127471196 127472363 255,0,0 ...
my question(s) is(are): Is this this the right way to get commonly bound regions by two factors? instead of directly printing the result on the screen, could I wrap them up to an output bed.file? (I searched the bedtools manual, but to no avail.) Thanks in advance.