Hi-C Loop Calling

Overview

This skill provides a minimal and efficient workflow for detecting chromatin loops from Hi-C data stored in .mcool format and preparing results for visualization in IGV. The key steps involved include:

• Refer to the Inputs & Outputs section to verify required files and output structure.
• Always prompt user for genome assembly used.
• Always prompt user for resolution used to call loops. ~2-50 kb is recommended. 5 kb is default.
• Locate the genome FASTA file from homer genome fasta file based on user input.
• Rename chromosomes in the .mcool or .cool file to satisfy the chromosome format with "chr".
• Generate chromosome-arm view files for compartment calling after changing the chromosome name.
• Extract contact matrices from .mcool files at the desired resolution.
• Detect chromatin loops.

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When to Use This Skill

Use this skill when:

• You need to identify (in other words, call, or detect) chromatin loops from Hi-C data in .mcool format.

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Inputs & Outputs

Inputs

• File format: .mcool, .cool, or .hic (Hi-C data file).
• Genome assembly: Prompt the user for genome assembly used.
• Resolution: Choose the desired resolution for loop calling (e.g., 5 kb, 10 kb, etc.).

Outputs

${sample}_loop_calling/
    loops/
        ${sample}_loops_${resolution}.bedpe  # Detected chromatin loops in BEDPE format.
    temp/
        view_${genome}.tsv
        expected_cis.${resolution}.tsv 

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Allowed Tools

When using this skill, you should restrict yourself to the following MCP tools from server cooler-tools, cooltools-tools, project-init-tools, genome-locate-tools:

• mcp__project-init-tools__project_init
• mcp__genome-locate-tools__genome_locate_fasta
• mcp__HiCExplorer-tools__hic_to_mcool
• mcp__cooler-tools__list_mcool_resolutions
• mcp__cooler-tools__harmonize_chrom_names
• mcp__cooler-tools__make_view_chromarms
• mcp__cooltools-tools__run_expected_cis
• mcp__cooltools-tools__run_dots

Do NOT fall back to:

• raw shell commands (cooltools expected-cis, cooltools dots, etc.)
• ad-hoc Python snippets (e.g. importing cooler, bioframe, matplotlib manually in the reply).

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Decision Tree

Step 0 — Gather Required Information from the User

Before calling any tool, ask the user:

1. Sample name (sample): used as prefix and for the output directory ${sample}_loop_calling.

2. Genome assembly (genome): e.g. hg38, mm10, danRer11.

   • Never guess or auto-detect.

3. Hi-C matrix path/URI (mcool_uri):

   • path/to/sample.mcool::/resolutions/5000 (.mcool file with resolution specified)
   • or .cool file path
   • or .hic file path

4. Resolution (resolution): default 5000 (5 kb).

   • If user does not specify, use 5000 as default.
   • Must be the same as the resolution used for ${mcool_uri}

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Step 1 — Initialize Project & Locate Genome FASTA

1. Make director for this project:

Call:

• mcp__project-init-tools__project_init

with:

• sample: the user-provided sample name
• task: loop_calling

The tool will:

• Create ${sample}_loop_calling directory.
• Return the full path of the ${sample}_loop_calling directory, which will be used as ${proj_dir}.

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2. If the user provides a .hic file, convert it to .mcool file using mcp__HiCExplorer-tools__hic_to_mcool tool:

Call:

• mcp__HiCExplorer-tools__hic_to_mcool

with:

• input_hic: the user-provided path (e.g. input.hic)
• sample: the user-provided sample name
• proj_dir: directory to save the view file. In this skill, it is the full path of the ${sample}_loop_calling directory returned by mcp__project-init-tools__project_init.

The tool will:

• Convert the .hic file to .mcool file.
• Return the path of the .mcool file.

If the conversion is successful, update ${mcool_uri} to the path of the .mcool file.

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3. Locate genome fasta file:

Call:

• mcp__genome-locate-tools__genome_locate_fasta

with:

• genome: the user-provided genome assembly

The tool will:

• Locate genome FASTA.
• Verify the FASTA exists.

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Step 2: List Available Resolutions in the .mcool file & Modify the Chromosome Names if Necessary

1. Check the resolutions in mcool_uri:

Call:

• mcp__cooler-tools__list_mcool_resolutions

with:

• mcool_path: the user-provided path (e.g. input.mcool) without resolution specified.

The tool will:

• List all resolutions in the .mcool file.
• Return the resolutions as a list.

If the user defined or default ${resolution} is not found in the list, ask the user to specify the resolution again. Else, use ${resolution} for the following steps.

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2. Check if the chromosome names in the .mcool file are started with "chr", and if not, modify them to start with "chr":

Call:

• mcp__cooler-tools__harmonize_chrom_names

with:

• sample: the user-provided sample name
• proj_dir: directory to save the expected-cis and eigs-cis files. In this skill, it is the full path of the ${sample}_Compartments_calling directory returned by mcp__project-init-tools__project_init
• mcool_uri: cooler URI with resolution specified, e.g. input.mcool::/resolutions/${resolution}
• resolution: ${resolution} must be the same as the resolution used for ${mcool_uri} and must be an integer

The tool will:

• Check if the chromosome names in the .mcool file.
• If not, harmonize the chromosome names in the .mcool file.
• If the chromosome names are modified, return the path of the modified .mcool file under ${proj_dir}/ directory

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Step 3 — Create Chromosome-Arm View File

Use bioframe to define chromosome arms based on centromeres:

Call:

• mcp__cooler-tools__make_view_chromarms

with:

• genome: genome assembly
• mcool_uri: cooler URI with resolution specified, e.g. input.mcool::/resolutions/${resolution}
• resolution: ${resolution} must be the same as the resolution used for ${mcool_uri} and must be an integer
• proj_dir: directory to save the view file. In this skill, it is the full path of the ${sample}_loop_calling directory returned by mcp__project-init-tools__project_init.

The tool will:

• Fetch chromsizes and centromeres via bioframe.
• Generate chromosomal arms and filter them to those present in the cooler.
• Return the path of the view file under ${proj_dir}/temp/ directory.

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Step 4: Detect Chromatin Loops

1. Calculate expected cis:

Call:

• mcp__cooltools-tools__run_expected_cis

with:

• sample: the user-provided sample name
• proj_dir: directory to save the view file. In this skill, it is the full path of the ${sample}_loop_calling directory returned by mcp__project-init-tools__project_init.
• mcool_uri: cooler URI with resolution specified, e.g. input.mcool::/resolutions/${resolution}
• resolution: ${resolution} must be the same as the resolution used for ${mcool_uri} and must be an integer
• view_path: the path to the view file (e.g. ${proj_dir}/temp/view_${genome}.tsv)
• clr_weight_name: the name of the weight column (default: weight)
• ignore_diags: the number of diagonals to ignore based on resolution

The tool will:

• Generate expected cis file.
• Return the path of the expected cis file under ${proj_dir}/temp/ directory.

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2. Call loops:

Call:

• mcp__cooltools-tools__run_dots

with:

• sample: the user-provided sample name
• proj_dir: directory to save the view file. In this skill, it is the full path of the ${sample}_loop_calling directory returned by mcp__project-init-tools__project_init.
• mcool_uri: cooler URI with resolution specified, e.g. input.mcool::/resolutions/${resolution}
• resolution: ${resolution} must be the same as the resolution used for ${mcool_uri} and must be an integer
• view_path: the path to the view file (e.g. ${proj_dir}/temp/view_${genome}.tsv)
• nproc: the number of processes for cooltools (default 6)

The tool will:

• Generate loops bedpe.
• Return the path of the loops bedpe file under ${proj_dir}/loops/ directory.

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