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track-generation

@BIsnake2001/ChromSkills
3
0

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`).

Install Skill

1Download skill
2Enable skills in Claude

Open claude.ai/settings/capabilities and find the "Skills" section

3Upload to Claude

Click "Upload skill" and select the downloaded ZIP file

Note: Please verify skill by going through its instructions before using it.

SKILL.md

name track-generation
description 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`).

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