Claude-skill-registry hic-tad-calling

This skill should be used when users need to identify topologically associating domains (TADs) from Hi-C data in .mcools (or .cool) files or when users want to visualize the TAD in target genome loci. It provides workflows for TAD calling and visualization.

install

source · Clone the upstream repo

git clone https://github.com/majiayu000/claude-skill-registry

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/majiayu000/claude-skill-registry "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/data/18-toolbased-hic-tad-calling" ~/.claude/skills/majiayu000-claude-skill-registry-hic-tad-calling && rm -rf "$T"

manifest: skills/data/18-toolbased-hic-tad-calling/SKILL.md

source content

TADs Calling with HiCExplorer and Cooltools

Overview

This skill enables comprehensive identification and analysis of topologically associating domains (TADs) from Hi-C data stored in .mcool (or .cool) files. It integrates HiCExplorer for robust TAD calling and visualization capabilities.

Main steps include:

Refer to the Inputs & Outputs section to verify required files and output structure.
Data Preparation: Ensure .mcool files are formatted correctly and resolutions are verified.
Always prompt user for resolution used to call TADs.
TAD Calling: Use HiCExplorer to call TADs with customizable parameters.
Always prompt user for target genomic loci for visualization.
Visualization: Generate contact maps with TAD boundaries overlayed, for specific regions of the genome.

When to use this skill

Use this skill when:

You need to identify TADs in Hi-C data stored in .mcool (or .cool) files.
You want to visualize TADs in a specific region of the genome.
You need to perform automated TAD calling with HiCExplorer, including statistical corrections.

Inputs & Outputs

Inputs

File format: .mcool, .cool, or .hic (Hi-C data file).
Resolution: Provided by user. ~10-50 kb is recommended. Default is 50 kb. 25 kb is the best but memory-consuming.
Target region: Genome region provided by user to visualize TADs (e.g.,
```
"chr22:1000000-2000000"
```
).

Outputs

${sample}_TAD_calling/
    TADs/
        ${sample}_TAD_boundaries.bed  # Called TADs in BED format
        ${sample}_TAD_boundaries.gff
        ${sample}_TAD_domains.bed
        ... # other files output by the hicFindTADs
    plots/
        ${sample}_TADs_${genome_loci}.pdf  # TADs visualization (contact map)
    temp/
        ${sample}_track.ini            # Configuration file for visualization

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__HiCExplorer-tools__check_mcool_file

```
mcp__HiCExplorer-tools__run_hicFindTADs
```

mcp__HiCExplorer-tools__generate_track_ini

mcp__HiCExplorer-tools__plot_tads_region

Do NOT fall back to:

raw shell commands (
```
hicFindTADs
```
,
```
hicPlotTADs
```
, etc.)
ad-hoc Python snippets (e.g. importing
```
cooler
```
,
```
bioframe
```
,
```
matplotlib
```
manually in the reply).

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}_TAD_calling
```
.
Genome assembly (
```
genome
```
): e.g.
```
hg38
```
,
```
mm10
```
,
```
danRer11
```
.
- Never guess or auto-detect.
Hi-C matrix path/URI (
```
mcool_uri
```
): e.g.
```
.mcool
```
file path or
```
.hic
```
file path.
- ```
path/to/sample.mcool::/resolutions/50000
```
  (.mcool file with resolution specified)
- or
```
.cool
```
  file path
- or
```
.hic
```
  file path
Resolution (
```
resolution
```
): default
```
50000
```
(50 kb).
- If user does not specify, use
```
50000
```
  as default.
- Must be the same as the resolution used for
```
${mcool_uri}
```

Step 1: Initialize Project

Make director for this project:

Call:

```
mcp__project-init-tools__project_init
```

with:

```
sample
```
: the user-provided sample name
```
task
```
: TAD_calling

The tool will:

Create
```
${sample}_TAD_calling
```
directory.
Get the full path of the
```
${sample}_TAD_calling
```
directory, which will be used as
```
${proj_dir}
```
.

If the user provides a
```
.hic
```
file, convert it to
```
.mcool
```
file first 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}_TAD_calling
```
directory returned by
```
mcp__project-init-tools__project_init
```
.
```
resolutions
```
: the user-provided resolutions (e.g.
```
[50000]
```
)

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.

Inspect the
```
.mcool
```
file 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
```
.mcool
```
file returned by
```
mcp__HiCExplorer-tools__hic_to_mcool
```

The tool will:

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

If the

${resolution}

is not found, ask the user to specify the resolution again. Else, use

${resolution}

Step 2: HiCExplorer TAD Calling

Use

mcp__HiCExplorer-tools__run_hicFindTADs

for comprehensive TAD identification. Customize parameters to suit the resolution and depth of your Hi-C data: Before calling the tool, ask the user for the following parameters:

```
${min_depth}
```
: Minimum window size (e.g. 3x resolution, default 150000, must be at least 3 times larger than the resolution)
```
${max_depth}
```
: Maximum window size (e.g. 6-10x resolution, default 300000, must be at least 5 times larger than the resolution)
```
${step}
```
: Step size for sliding window (default 50000, 25000 is the best but memory-consuming)
```
${multiple_testing}
```
: Multiple testing correction method (e.g. 'fdr')
```
${threshold_comparisons}
```
: FDR threshold for significant TADs (default 0.05)
```
${delta}
```
: Delta parameter for TAD boundary detection (default 0.01)
```
${chromosomes}
```
: Chromosomes to call TADs (default
```
chr22
```
). It is suggested to call TADs on a certain chromosome because it is memory-consuming to call TADs on all chromosomes and this process would likely be killed by the system.

Call:

```
mcp__HiCExplorer-tools__run_hicFindTADs
```
with:
```
sample
```
:
```
${sample}
```
```
proj_dir
```
: directory to save the view file. In this skill, it is the full path of the
```
${sample}_TAD_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
```
min_depth
```
:
```
${min_depth}
```
, must be at least 3 times larger than the resolution.
```
max_depth
```
:
```
${max_depth}
```
, must be at least 5 times larger than the resolution.
```
step
```
:
```
${step}
```
```
multiple_testing
```
:
```
${multiple_testing}
```

threshold_comparisons

${threshold_comparisons}

```
delta
```
:
```
${delta}
```
```
chromosomes
```
: chromosomes to call TADs, e.g.
```
chr22
```
, space-separated list.

The tool will:

Call
```
mcp__HiCExplorer-tools__run_hicFindTADs
```
to identify TADs.
Return the path of the TADs file under
```
${proj_dir}/TADs/
```
directory.

Step 3: Visualization

generate the
```
<track.ini>
```
file first for visualization

Call:

mcp__HiCExplorer-tools__generate_track_ini

with:

```
sample
```
:
```
${sample}
```
```
proj_dir
```
: directory to save the view file. In this skill, it is the full path of the
```
${sample}_TAD_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
```
depth
```
: depth for the Hi-C matrix view, e.g. 1500000
```
min_value
```
: minimum value for the Hi-C matrix view, e.g. 0.0
```
max_value
```
: maximum value for the Hi-C matrix view, e.g. 80.0

The tool will:

Generate the
```
<track.ini>
```
file under
```
${proj_dir}/temp/
```
directory.
Return the path of the
```
<track.ini>
```
file.

Contact Maps with TAD Overlays Before calling the tool, ask the user for the target region, like
```
"chr22:1000000-2000000"
```
.

Call:

mcp__HiCExplorer-tools__plot_tads_region

with:

```
sample
```
:
```
${sample}
```
```
proj_dir
```
: directory to save the view file. In this skill, it is the full path of the
```
${sample}_TAD_calling
```
directory returned by
```
mcp__project-init-tools__project_init
```
.
```
region
```
: user-provided target region, like
```
"chr22:1000000-2000000"
```
```
dpi
```
: dpi for the contact map, default is 300

The tool will:

Generate the contact map with TAD boundaries overlayed.
Return the path of the contact map file under
```
${proj_dir}/plots/
```
directory.

Best Practices

It is suggested to call TADs on a certain chromosome because it is memory-consuming to call TADs on all chromosomes and this process would likely be killed by the system.