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alignment-level-QC

Calculate alignment-level QC metrics for ChIP-seq and ATAC-seq BAM files.

12|3|Updated Nov 4, 2025
Search Tags:#alignment#quality-control#bam#qc#samtools#picard#multiqc
One-click install
npx skills add https://github.com/BIsnake2001/ChromSkills --skill alignment-level-qc
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alignment-level-QC
Source: https://github.com/BIsnake2001/ChromSkills/tree/main/1.alignment-level-QC
Command: npx skills add https://github.com/BIsnake2001/ChromSkills --skill alignment-level-qc

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This skill performs comprehensive alignment-level quality control for ChIP-seq and ATAC-seq BAM files, validating sorting, read groups, and overall mapping quality, and producing a MultiQC report to flag issues before downstream analyses.

Core Features & Use Cases

  • Initialize the project directory structure under ${proj_dir} and prepare outputs.
  • Check and fix BAM files by adding missing Read Groups, sorting, and indexing as needed.
  • Run alignment QC metrics (flagstat, stats, insertsize, dup metrics) and generate a consolidated MultiQC report for per-sample quality assessment.

Quick Start

Run the alignment-level-QC workflow on a BAM file to generate per-sample QC metrics and a MultiQC report.

Frequently Asked Questions about alignment-level-QC

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run alignment QC on ChIP-seq and ATAC-seq BAM files?▼

Alignment QC for ChIP-seq and ATAC-seq BAM files is performed by validating sorting and read groups, computing metrics with samtools and Picard, and generating a consolidated MultiQC report under the project directory.

What is the best way to check BAM formatting and read groups before downstream analysis?▼

Checking BAM formatting and read groups requires validating sorting and indexing status, adding missing Read Groups, and running flagstat and stats to ensure mapping quality before downstream analyses.

Can I use samtools and Picard to fix missing read groups in BAM files?▼

Yes, samtools and Picard can check and fix BAM files by adding missing Read Groups, sorting, and indexing as needed to prepare them for reliable alignment QC metric computation.

How does MultiQC consolidate alignment QC metrics for multiple samples?▼

MultiQC consolidates alignment QC metrics by aggregating flagstat, stats, insert size, and duplication metrics into a single comprehensive report for per-sample quality assessment.

Do I need to sort and index BAM files before running alignment-level QC?▼

Sorting and indexing BAM files are required steps handled during pre-processing; the workflow checks formatting, fixes sorting and indexing, and adds Read Groups before computing QC metrics.

Why does alignment-level QC flag issues in BAM files before downstream analysis?▼

Alignment-level QC flags issues by validating BAM formatting, read groups, and mapping quality to prevent unreliable data from entering downstream ChIP-seq and ATAC-seq analyses.

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