Hi, I am doing super enhancer analysis with ROSE. I wonder whether the ROSE software can give the information of traditional enhancers or enhancers that make up SEs.
Thanks
Yes, pretty much any of the files with "AllEnhancers.table.txt" have that information as to which enhancers are super enhancers or not in the last "isSuper" column. Those with a 1 are super enhancers, those with a 0 are "typical" enhancers.
If you're just looking for the constituent peaks that compose each SE, I'd just do a bedtools intersect of the input peaks and SE outputs.
Yes, I am looking for the constituent peaks for the SE and other traditional enhancers. This is really helpful. Thanks for the suggestion of using the bedtools.
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