I am attempting to identify DNA sequences/regions associated with enhancers in my NGS sequencing data. How can I identify (from peak files/counts for chip-seq, atac etc.) genomics regions/peaks associated with enhancers? I know proximity to genes and possibly histone (i.e. h3k27ac) activity near known genes is possibly an indicator, but is this the only way and how is the computational process formalized/captured? What are the specific set of tools involved? i.e. Peak annotations etc.? Thank you.
As I understand it in my limited bio knowledge, enhancers are at varying distances from genes and sometimes they are multiples (super-enhancers). Are all enhancers already "known/described" (akin to genes)? What is/was the process of finding them (human manual procedure)? It's that more manual/heuristic process (without ML) I am looking for so we can consider formalizing and automating it.
Based on a very insightful answer: I think some input/clarity on the following bit would make the answer(s) even more valuable:
Possible list of steps towards this include following tools/functions:
Bowtie (to align fastq to a genome, mouse, human etc.)
Homer/makeTagDirectory (Sep files, associate chr/coords with tags/sequence reads)
Homer/findPeaks (identify and list genomic regions/sequences with count values above a threshold)
Homer/pos2bed (convert peaks to bed file, genome browser compatible form)
Homer/annotatePeaks.pl (Runs on *bed file - Don't know much about this, but intuitively associate a label with peaks found in 4?)
Question: Is there a step 6? Where do we go after annotatedPeaks for example to get to enhancers?