I did ChIP seq using H3K27ac antibody to quantify super enhancer regions in normal vs breast cancer cells. I ran ROSE algorithm on normal mammary epithelial cells and breast cancer cells to get a list of super enhancer regions in each cell line. I have a list of super enhancer regions for both and I want to compare super enhancers between the two outputs I got. How would i compare the two lists and see if they have super enhancer regions that overlap or not to analyze acquired/lost super enhancers between the two cell lines. I know bedtools intersect might be able to do it, but am confused about the command I would input to compare the two files. Any help is appreciated. Thank you
Not sure I grasp the full scope of the issue, but a typical
bedtools intersect command would simply go like this:
bedtools intersect -a super_enhancer_list-A.bed -b super_enhancer_list-B.bed > super_enhancers_from_A_that_are_also_in_B.bed
From personal experience, I recommend that you compare signal for the constituent peaks rather than the entire SE, as differences for such large regions tend to get muddled due to the peak stitching inherent in the SE calling process.