juicer-cli-tool-execution

juicer-cli-tool-execution

Summary

Execute Juicer command-line tools to annotate structural features (loops, domains) on pre-generated .hic contact maps. This skill bridges the gap between raw Hi-C map generation and downstream feature discovery by applying Juicer's post-processing CLI suite to identify and output genomic loop coordinates and topologically associating domain (TAD) boundaries.

When to use

You have a pre-generated .hic contact map file (from Juicer pipeline or external source) and need to systematically call chromatin loops, detect topologically associating domains, or annotate other structural features without re-running the full alignment and contact matrix construction pipeline. This skill is appropriate when Hi-C data has already been processed to the contact map stage and feature annotation is the isolated requirement.

When NOT to use

• Input is raw FASTQ sequence data—use the Juicer pipeline generation step first to create the .hic file.
• Contact map already includes feature annotations—re-annotation risks overwriting or conflicting with existing calls.
• Analysis requires real-time interaction with the map visualization—use Juicebox (the GUI) instead of CLI tools for exploratory work.

Inputs

• .hic contact map file (pre-generated from Juicer pipeline or compatible source)
• genome identifier or reference file (e.g., 'hg19', 'mm10', or custom chrom.sizes)
• tool-specific parameters (e.g., resolution, p-value thresholds, GPU availability for HiCCUPS)

Outputs

• annotated feature file in bedpe format (for loop coordinates: chr1, start1, end1, chr2, start2, end2, feature_id, score)
• annotated feature file in bed format (for domain boundaries: chr, start, end, domain_id, score)
• optional: feature statistics or confidence scores

How to apply

Load the .hic file into Juicer command-line tools (which require Java >= 1.8 installed). Select the appropriate post-processing tool from the CLI suite—common tools include HiCCUPS for loop calling or Arrowhead for domain detection. Execute the chosen annotation tool with the .hic file as primary input, specifying kilobase resolution and any tool-specific parameters (e.g., peak-calling thresholds for HiCCUPS). The tool will scan the contact matrix for statistically significant peaks or domain boundaries and output results in a standardized coordinate format (typically bedpe for loops or bed for domains). Validate output by checking coordinate consistency with input map dimensions and confirming feature counts align with biological expectations for the organism and resolution.