loop-annotation

What problem does it solve?

This skill annotates chromatin loops for Hi-C/HiChIP/ChIA-PET data, assigning enhancers, promoters, and CTCF overlaps, and can auto-create missing enhancer and promoter sets for complete loop context.

Core Features & Use Cases

• Build enhancers.bed and promoters.bed if missing, using ATAC/H3K27ac and gene annotations.
• Standardize loops input (bedpe) for downstream HOMER-based annotation.
• Generate annotated loop categories and visualizations to support regulatory loop analyses.

Quick Start

Provide the required inputs (loops.bedpe, ctcf_peaks.bed, and genome) and run the loop-annotation workflow to generate annotated loop categories and visualizations.