القائمة
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.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
| 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. |
This skill performs Hi-C data normalization on .mcool files.
Main steps include:
Use the hic-normalization pipeline when:
This tool assumes the file already has correct genome assembly and chromosome names.
${sample}_hic_norm/
${sample}_norm.mcool
normalization_report.txt # A brief log/report indicating which resolutions were detected, normalized, or skipped.
Before calling any tool, ask the user:
sample): used as prefix and for the output directory ${sample}_hic_norm.genome): e.g. hg38, mm10, danRer11.
mcool_path): e.g. .mcool file path or .hic file path.
path/to/sample.mcool (.mcool file without resolution specified).hic file pathCall:
mcp__project-init-tools__project_initwith:
sample: the user-provided sample nametask: hic_normThe tool will:
${sample}_hic_norm directory.${sample}_hic_norm directory, which will be used as ${proj_dir}..hic file, convert it to .mcool file first using mcp__HiCExplorer-tools__hic_to_mcool tool:Call:
mcp__HiCExplorer-tools__hic_to_mcoolwith:
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_norm directory returned by mcp__project-init-tools__project_init.resolutions: the user-provided resolutions (e.g. [50000])The tool will:
.hic file to .mcool file..mcool file.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.
.mcool file to list available resolutions and confirm the analysis resolution with the user.Call:
mcp__cooler-tools__list_mcool_resolutionswith:
mcool_path: the user-provided path (e.g. input.mcool) or the path of the .mcool file returned by mcp__HiCExplorer-tools__hic_to_mcoolThe tool will:
Call:
mcp__cooler-tools__check_and_balance_mcoolwith:
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, run cooler.balance_cooler on 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_diags in cooler.balance_cooler)mad_max: the mad_max parameter for cooler.balance_cooler (default: cooler's own)converge: the convergence tolerance, maps to tol in cooler.balance_coolermax_iters: the max_iters parameter for cooler.balance_coolercis_only: if true, balance cis contacts only (cis_only=True)The tool will:
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