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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.
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Basado en la clasificación ocupacional SOC
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| 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:
${proj_dir}/ directory.