A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

This protocol provides a streamlined computational pipeline for quantifying nascent enhancer transcripts. By integrating chromatin accessibility, chromatin feature, and transcriptional data, it enables accurate detection and strand-specific analysis of enhancer activity in complex intragenic regions, while remaining accessible to researchers without extensive bioinformatics training.