chromatin-domain-boundary-detection

chromatin-domain-boundary-detection

Summary

Detect chromatin domain boundaries (TADs and other structural domains) on kilobase-resolution Hi-C contact maps using Juicer command-line feature annotation tools. This skill applies domain-detection algorithms to pre-generated .hic files to identify and output domain boundary coordinates.

When to use

You have generated a .hic contact map from Hi-C raw sequencing data and need to identify topologically associating domains (TADs) or other chromatin structural boundaries. Apply this skill when your analysis goal is to map the physical boundaries of self-interacting chromatin regions at kilobase resolution, typically as a post-processing step after Hi-C map generation.

When NOT to use

• Input is raw FASTQ sequencing data — the Hi-C map must be pre-generated first using the Juicer pipeline.
• You only need loop-level features (e.g., enhancer–promoter loops) rather than domain-level structure — use loop-calling tools instead.
• Your contact map is at single-cell or very low resolution where domain structure is not reliably detectable.

Inputs

• .hic contact map file (pre-generated from aligned Hi-C data)
• genome identifier (e.g., 'hg19', 'mm10')

Outputs

• Domain boundary coordinate file (e.g., domain list with chromosome, start, end positions)
• Annotated feature file in format specified by domain-detection tool

How to apply

Load the pre-generated .hic contact map file into Juicer command-line tools, which provide a suite of post-processing feature annotation tools including domain-detection algorithms. Select and execute the appropriate domain-detection command from the Juicer CLI (e.g., arrowhead or other domain-calling methods available in juicer_tools). The algorithm analyzes the contact frequency patterns in the Hi-C matrix to identify boundaries where inter-domain contacts drop sharply. Execute the tool with parameters appropriate to your resolution and genome; the tool outputs domain boundary coordinates in a structured format (e.g., BED-like or coordinate list). Validate output by comparing domain sizes and boundaries against known TAD structures or by visual inspection in Juicebox.