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Track Generation

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track-generation

Track Generation is an Agent Skill for documents published in the majiayu000/claude-skill-registry repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

This skill generates normalized BigWig (.bw) tracks (and/or fold-change tracks) from BAM files for ATAC-seq and ChIP-seq visualization. It handles normalization (RPM or fold-change) and Tn5 offset correction automatically. Use this skill when you have filtered and generated the clean BAM file (e.g. `*.filtered.bam`).

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How to use this skill

Bring this guide into your coding agent with a prompt tailored to the tool you use.

  1. Open your project in Codex.
  2. Copy and paste the prompt below.
  3. Review files and risks before approving any action.
Prompt to paste
Inspect the Agent Skill at https://github.com/majiayu000/claude-skill-registry/blob/HEAD/skills/data/6-track-generation-bisnake2001-chromskills/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/track-generation, but wait for my approval before writing files or running scripts.

Copying this prompt does not install or run the skill. Review third-party files before use.

Overview

This skill converts filtered BAM files into normalized signal tracks (BigWig) for genome browser visualization.
It supports both ATAC-seq and ChIP-seq datasets, automatically detecting genome assembly and chromosome size files.

Main steps include:

  • Refer to the Inputs & Outputs section to check inputs and build the output architecture. All the output file should located in ${proj_dir} in Step 0.
  • Always use filtered BAM file (*.filtered.bam) if available.
  • Normalize all tracks to 1 million mapped reads (RPM normalization).
  • Generate the chrom.size file.
  • For ATAC-seq, apply Tn5 offset correction (+4/−5) and generate normalized BigWig (RPM).
  • For ChIP-seq, generat RPM-normalized track without applying Tn5 offset correction

Decision Tree

Step 0: Initialize Project

Call:

  • mcp__project-init-tools__project_init

with:

  • sample: all
  • task: track_generation

The tool will:

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

Step 1: Generate Chromosome size file

Call:

  • mcp__bw-tools__generate_chrom_sizes with:
  • bam_file: Path for the BAM file for generating bigWig Tracks
  • output_path: ${proj_dir}/temp/${sample}.chrom.sizes

Step 2: Calculate Scaling Factor

Call:

  • mcp__bw_tools__calculate_scaling_factor with: bam_file: Path for the BAM file for generating bigWig Tracks

This step will store result as variable ${scale_factor}

Step 3: Create RPM-normalized BigWig scaled to 1M mapped reads.

  • (Option 1) For ATAC-seq data: Apply the standard Tn5 shift (+4/-5bp)

Call:

  • mcp__bw_tools__bam_to_bigwig with: bam_file: ${bam_file} chrom_sizes: ${proj_dir}/temp/${sample}.chrom.sizes (from Step 2) output_bw: ${proj_dir}/tracks/${sample_name}.RPM.bw scale_factor: ${scale_factor} shift_tn5: True temp_dir: ${proj_dir}/temp

  • (Option 2) For ChIP-seq data: Do Not Apply the standard Tn5 shift by setting shift_tn5 as False