alignment-level-QC
Calculates technical mapping statistics for any aligned BAM file (ChIP or ATAC). It assesses the performance of the aligner itself by generating metrics on read depth, mapping quality, error rates, and read group data using samtools and Picard.Use this skill to check "how well the reads mapped" or to validate BAM formatting/sorting before further processing. Do NOT use this skill for biological signal validation (like checking for peaks or open chromatin) or for filtering/removing reads.
npx skills add majiayu000/claude-skill-registry --skill 1-alignment-level-qc-bisnake2001-chromskills-2 --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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. --- ## Inputs & Outputs ### Inputs <sample>.bam ### Outputs ```bash alignment_qc/ ${sample}.bam # Original input ${sample}.sorted.bam # (Optional) Created if sorting was needed ${sample}.RG.bam # (Optional) Created if RG was needed ${sample}.RG.bam.bai # Index file qc_results/ ${sample}.flagstat.txt ${sample}.stats.txt ${sample}.insertsize_metrics.txt ${sample}.dup_metrics.txt alignment_qc_report.html # Visual MultiQC report qc_summary.txt # Pass/Warn/Fail table temp/ ${sample}.markdup.bam # Intermediate file (safe
- Overview
- When to use this skill
- Inputs & Outputs
- Inputs
- Outputs
- Decision Tree
- Step 0: Initialize Project
- Step 1: Check and Fix BAMs
- Step 2: Run Alignment QC Metrics
- Quality Assessment
- Key QC Metrics
- Quality Thresholds
- Report Generation
- Resources
alignment_qc/ qc_results/ alignment_qc_report.html # Visual MultiQC report qc_summary.txt # Pass/Warn/Fail table temp/
What does the alignment-level-QC skill do?
Calculates technical mapping statistics for any aligned BAM file (ChIP or ATAC). It assesses the performance of the aligner itself by generating metrics on read depth, mapping quality, error rates, and read group data using samtools and Picard.Use this skill to check "how well the reads mapped" or to validate BAM formatting/sorting before further processing. Do NOT use this skill for biological signal validation (like checking for peaks or open chromatin) or for filtering/removing reads.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 1-alignment-level-qc-bisnake2001-chromskills-2 --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.