Intersecting Encode peaks to search for tissue specific peaks?
As per the title, I have a list of H3K27ac peaks from my lab, and I would like to find out which of those are specific to my organ of interest. What I’ve decided to do was to download a set of H3k27ac peaks (bed files) from the ENCODE website and use bedtools intersect to find peaks that are not present in ENCODE data. But I have a feeling that I’m overlooking something, and I’m not too sure if this is the correct or appropriate way of doing this?
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