track-generationSafety --Repository ShareFavorite skill

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
• Always prompt user for whether need to visualize the signal profiles around TSS or target regions.
• Visualize the signal profiles around TSS or target regions if users require.

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

Step 3: Visualize the signal profiles around TSS or target region (Optional)

Call:

• mcp__bw_tools__visualize_signal_profile with: regions_bed: GTF (for gene tss) or BED file (for target regions), always query user for this file if not provided. signal_files: Input BigWig signal files. output_prefix: Output prefix for matrix/plots. reference_point: use TSS for genes, and center for target regions. upstream: Upstream distance (bp). downstream: Downstream distance (bp).