Alignment Quality Control for ChIP-seq/ATAC-seq

Overview

Perform comprehensive preliminary alignment-level quality control for ChIP-seq and ATAC-seq BAM files using samtools, Picard, and MultiQC.

Main steps include:

• Initialize the project directory.
• 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.
• Sort and add read groups if missing in the BAM file.
• Run preliminary QC metrics
• Generate MultiQC report

When to use this skill

• Use skill when you want to perform alignment-level quality control for ChIP-seq or ATAC-seq BAM files.