ATAC-seq Quality Control

Overview

This skill performs complete ATAC-seq data quality control from BAM and peak 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 prompt user for genome assembly used. Never decide by yourself.
• Generate TSS files according to genome assembly.
• Compute TSS enrichment, fragment distribution and FRiP.

Inputs & Outputs

Inputs

${sample}.bam # filtered bam files
${sample}.narrowPeak

Outputs

all_atac_qc/
    ${sample}_qc_results/
        ataqv_metrics.json
        ataqv_report.html/
    temp/

Decision Tree

Step 0: Initialize Project

Call:

• mcp__project-init-tools__project_init

with:

• sample: all
• task: atac_qc
• genome: provided by user

The tool will:

• Createall_atac_qc directory.
• Return the full path of the all_atac_qc directory, which will be used as ${proj_dir}.

Step 1: Detect the name logic of the chromosomes in BAM file (have "chr" as prefix or not)

samtools view <sample>.bam | head -n 10 | cut -f 3

Step 2: Generate reference files

Call:

• mcp__qc-tools__generate_reference

with:

• genome: Genome name (e.g., hg38), provided by user
• temp_dir: ${proj_dir}/temp
• bam_uses_chr: True if BAM uses 'chr' prefix (chr1), False if not (1).

Step 3: Peform quality control for the ATAC-seq data

Call:

• mcp__qc-tools__run_ataqv_qc

• bam_file: Path to filtered BAM file

• peak_file: Path to peak file (narrowPeak) corresponding to the BAM file

• tss_file: ${proj_dir}/temp/${genome}.tss

• species: Species used, choose from (fly, human, mouse, rat, worm, yeast)

• bam_uses_chr: True if BAM uses 'chr' prefix (chr1), False if not (1).

• output_dir: ${proj_dir}/${sample}_qc_results

• autosomal_ref_path: Provided if bam_uses_chr is False, ${proj_dir}/temp/${genome}.autosomal.ref