bisnake2001/hic-normalization
16_toolBased.hic-normalization/SKILL.md
Automatically detect and normalize Hi-C data. Only .cool or .mcool file is supported. All .mcool files are then checked for existing normalization (supports bins/weight only) and balanced if none of the normalizations exist.
$ install --global
skillsauthnpx skillsauth add bisnake2001/chromskills hic-normalizationInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- hic-normalization
- description:
- Automatically detect and normalize Hi-C data. Only .cool or .mcool file is supported. All .mcool files are then checked for existing normalization (supports bins/weight only) and balanced if none of the normalizations exist.
Overview
This skill performs Hi-C data normalization on .mcool files.
Main steps include:
- Refer to the Inputs & Outputs section to verify required files and output structure.
- Check normalization status per resolution (supports bins/weight columns only).
- If a resolution is not normalized, perform normalization with cooler balance (ICE) to create bins/weight.
- Verify normalization and emit a concise report on the file, resolution, and normalization status.
When to use this skill
Use the hic-normalization pipeline when:
- You need to ensure that Hi-C data is normalized for downstream analysis.
- Your data comes in .cool or .mcool formats, and you want to check or refresh normalization status (ICE normalization).
This tool assumes the file already has correct genome assembly and chromosome names.
Inputs & Outputs
Inputs
- Accepted file format: .mcool
Outputs
${sample}_hic_norm/
${sample}_norm.mcool
normalization_report.txt # A brief log/report indicating which resolutions were detected, normalized, or skipped.
Decision Tree
Step 0 — Gather Required Information from the User
Before calling any tool, ask the user:
- Sample name (
sample): used as prefix and for the output directory${sample}_hic_norm. - Genome assembly (
genome): e.g.hg38,mm10,danRer11.- Never guess or auto-detect.
- Hi-C matrix path (
mcool_path): e.g..mcoolfile path or.hicfile path.path/to/sample.mcool(.mcool file without resolution specified)- or
.hicfile path
Step 1: Initialize Project
- Make director for this project:
Call:
mcp__project-init-tools__project_init
with:
sample: the user-provided sample nametask: hic_norm
The tool will:
- Create
${sample}_hic_normdirectory. - Get the full path of the
${sample}_hic_normdirectory, which will be used as${proj_dir}.
- If the user provides a
.hicfile, convert it to.mcoolfile first usingmcp__HiCExplorer-tools__hic_to_mcooltool:
Call:
mcp__HiCExplorer-tools__hic_to_mcool
with:
input_hic: the user-provided path (e.g.input.hic)sample: the user-provided sample nameproj_dir: directory to save the view file. In this skill, it is the full path of the${sample}_hic_normdirectory returned bymcp__project-init-tools__project_init.resolutions: the user-provided resolutions (e.g.[50000])
The tool will:
- Convert the
.hicfile to.mcoolfile. - Return the path of the
.mcoolfile.
If the conversion is successful, update ${mcool_uri} to the path of the .mcool file. The ${mcool_path} should be updated to the path of the .mcool file without resolution specified.
- Inspect the
.mcoolfile to list available resolutions and confirm the analysis resolution with the user.
Call:
mcp__cooler-tools__list_mcool_resolutions
with:
mcool_path: the user-provided path (e.g.input.mcool) or the path of the.mcoolfile returned bymcp__HiCExplorer-tools__hic_to_mcool
The tool will:
- List all resolutions in the .mcool file.
- Return the resolutions as a list.
Step 2: Check Normalization Status (per resolution) on .mcool and normlize if missing
Call:
mcp__cooler-tools__check_and_balance_mcool
with:
sample: the user-provided sample nameproj_dir: the full path to the project directorymcool_path: the path to the .mcool file (e.g. input.mcool) without resolution specified.balance_missing: if true, runcooler.balance_cooleron resolutions missing /bins/weightstore_name: the name of the weight column to write into bins (default: 'weight')ignore_diags: the number of diagonals to ignore (ignore_diagsin cooler.balance_cooler)mad_max: themad_maxparameter for cooler.balance_cooler (default: cooler's own)converge: the convergence tolerance, maps totolin cooler.balance_coolermax_iters: themax_itersparameter for cooler.balance_coolercis_only: if true, balance cis contacts only (cis_only=True)
The tool will:
- Check the normalization status (per resolution) on the .mcool file.
- If the normalization is missing, balance the .mcool file.
- Return the path of the balanced .mcool file under
${proj_dir}/directory.
Notes & Troubleshooting
- Normalization fails to converge: Increase iterations or adjust the convergence criteria (--max-iters, --converge)
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