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
Of these, ChromHMM is probably the most widely used in publications at the moment.
Also see other answers on biostars on chromatin segmentation and enhancers:
I have not used any tools but an easy thing could be to do a overlap between e.g. H3K27ac and H3K4me1 and found the overlapping regions, these are the most likely enhancer marks. You can do a heatmap for H3K27ac peaks and compare the occurrence of H3K4me1 and H3K4me3 around these peaks. you can use seqMiner for producing a heatmap. Regions which are enriched with K27ac + K4me1 and Edited: absent or low K4me3 are most probable enhancer regions (if you have region annotation of these peaks, these will mostly be intergenic of intronic peaks). You need to call for H3K27ac peaks before the analysis.