Does ROSE include traditional enhancer in the analysis output?

Question

[b8921019]

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

Answer 1

[jared.andrews07]

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.

[b8921019]

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.