Claude-skill-registry hic-loop-calling

This skill performs chromatin loop detection from Hi-C .mcool files using cooltools.

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 "$T/skills/data/19-toolbased-hic-loop-calling" ~/.claude/skills/majiayu000-claude-skill-registry-hic-loop-calling && rm -rf "$T"

manifest: skills/data/19-toolbased-hic-loop-calling/SKILL.md

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.

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.

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

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).

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}_loop_calling
```
.
Genome assembly (
```
genome
```
): e.g.
```
hg38
```
,
```
mm10
```
,
```
danRer11
```
.
- Never guess or auto-detect.
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
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}
```

Step 1 — Initialize Project & Locate Genome FASTA

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}
```
.

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.

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.

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

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.

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

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.

Step 4: Detect Chromatin Loops

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.

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.