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:

• Create

  all_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