Compute TSS enrichment, fragment-size distributions, and FRiP from BAM and peak files.
npx skills add https://github.com/BIsnake2001/ChromSkills --skill atacseq-qc
Please help me install this Agent Skill. Skill: ATACseq-QC Source: https://github.com/BIsnake2001/ChromSkills/tree/main/4.ATACseq-QC Command: npx skills add https://github.com/BIsnake2001/ChromSkills --skill atacseq-qc
ATAC-seq experiments generate BAM alignments and peak calls; this skill provides automatic quality-control metrics to assess data quality, including TSS enrichment and fragment size distributions, enabling early detection of issues before downstream analysis. It is not intended for ChIP-seq data or general alignment statistics.
${proj_dir}/all_atac_qc/...) and the workflow prompts for genome assembly and uses peak files alongside BAMs.Initialize an ATAC-seq QC project with your filtered BAM and peak files, then run the QC workflow to produce per-sample metrics.
High-intent search queries and answers about installing and using this skill.
You can calculate TSS enrichment and FRiP from ATAC-seq BAM files by providing filtered BAM alignments and corresponding peak files to compute quality metrics using the ataqv toolchain. It generates genome-specific TSS references and structured QC reports.
To assess ATAC-seq library complexity, you should check fragment-size distributions and nucleosome patterning. This Skill calculates these metrics alongside TSS enrichment and FRiP scores to help detect low complexity or poor library preparation issues early.
No, you cannot use this ATAC-seq QC workflow for ChIP-seq data or general alignment statistics. It is strictly designed to quantify ATAC-seq data quality by computing TSS enrichment, fragment-size distributions, and FRiP from BAM and peak files.
To generate a multi-sample ATAC-seq QC report, initialize a project directory with your filtered BAM and peak files, specify the genome assembly, and run the workflow. It processes single or multi-sample projects and outputs structured results under the project directory.
Yes, you need to prepare filtered BAMs and corresponding peak files before running ATAC-seq quality control. The workflow requires these pre-processed inputs to accurately compute TSS enrichment, fragment-size distributions, and FRiP metrics across your samples.
The ATAC-seq QC workflow prompts you for the genome assembly and automatically generates genome-specific TSS reference files. This ensures accurate TSS enrichment calculation tailored to your specific organism's transcription start site coordinates.
BIsnake2001Automate peak calling from BAM files for ChIP-seq and ATAC-seq experiments.
MDheweiAnnotate ATAC-seq or ChIP-seq peaks with genomic context and QC metrics.
ovachieverConvert BAM alignments into normalized coverage tracks and generate QC metrics.
LeonChaoXConvert BAM alignment files into normalized genome coverage tracks and perform QC.