Hi there,

I’m looking for help on how to access enhancer regions from ENCODE annotation files. I’m researching the enhancers in the human heart.

I planned to download enhancer regions from the ENCODE database. I downloaded 49 files from this search: https://www.encodeproject.org/encyclopedia/?type=File&annotation_type=candidate+Cis-Regulatory+Elements&assembly=GRCh38&file_format=bigBed&file_format=bigWig&biosample_ontology.organ_slims=heart&encyclopedia_version=ENCODE+v4&biosample_ontology.term_name=heart&biosample_ontology.term_name=heart+left+ventricle&biosample_ontology.term_name=heart+right+ventricle

In my understanding, the annotation .bigbed files I downloaded contain different kinds of cis-regulatory regions, such as promoters, enhancers, insulators (marked by CTCF binding), and others, but not only enhancers. I had a difficult time to understand the meaning of each column and couldn’t find enhancers. They are only labeled as "Low-DNase" and "Missing-data/Partial-classification."

Here’s an example of the first line of a bigbed file:

chr1      104896               105048               EH38E2776520             0             .              104896               105048                225,225,225   Low-DNase     Missing-data/Partial-classification

I wonder if there is any guidance to extract enhancer regions from these annotated bigwig/bed files? What are the column names of bigbed files?