Hello everyone,
I would like to know if there are tools that feeded with ChIP-seq data for various histone marks, identify the enhancers by the "right" methylation/acetylation combinations.
Until now, I found CSI-ANN, but I was wondering if there are other tools.
Thanks

The search term you're looking for is "chromatin segmentation". For example, omicstools has [a list of chromatin segmentation tools][1]

Of these, [ChromHMM][2] is probably the most widely used in publications at the moment.

Also see other answers on biostars on chromatin segmentation and enhancers:

 - https://www.biostars.org/p/185468
 - https://www.biostars.org/p/17912
 - https://www.biostars.org/p/175982
 - https://www.biostars.org/p/142111


  [1]: https://omictools.com/chromatin-segmentation-category
  [2]: http://compbio.mit.edu/ChromHMM/