Comprehensive ChIP-seq QC Pipeline

Overview

This skill performs a full ChIP-seq quality control analysis from aligned BAM files 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.
• Perform cross-correlation analysis to calculate NSC and RSC.
• Compute FRiP (Fraction of Reads in Peaks) using peak files and aligned BAMs.

---

Inputs & Outputs

Inputs

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

Outputs

all_chip_qc/
    ${sample}_spp.txt
    ${sample}_crosscorr.pdf
    ${sample}_frip.txt

---

Step 0: Initialize Project

Call:

• mcp__project-init-tools__project_init

with:

• sample

  : all

• task

  : atac_qc

The tool will:

• Create

  all_chip_qc

  directory.
• Return the full path of the

  all_chip_qc

  directory, which will be used as

  ${proj_dir}

  .

Step 1: Calculate Cross-Correlation Metrics (NSC, RSC)

Call:

• mcp__qc-tools__run_phantompeakqualtools with:

• bam_file

  : Path to BAM file

• output_dir

  : ${proj_dir}/

Output:

${sample}_spp.txt

,

${sample}_crosscorr.pdf

Step 2: Calculate the fraction of reads falling within peak regions.

Call:

• mcp__qc-tools__calculate_frip with: bam_file: Path to BAM file. peak_file: Path to Peak file (BED/narrowPeak/broadPeak). output_dir: ${proj_dir}/

Output:

${sample}_frip.txt