Automate ATAC-seq processing and peak calling from raw FASTQ reads.
npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-atacseq
Please help me install this Agent Skill. Skill: pipeline-atacseq Source: https://github.com/ammawla/encode-toolkit/tree/main/plugin/skills/pipeline-atacseq Command: npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-atacseq
This Skill streamlines the analysis of ATAC-seq data by providing an automated pipeline from raw sequencing reads to high-confidence accessible chromatin peaks, enabling accurate epigenomic insights.
Run the pipeline with your FASTQ files and reference genome to obtain peaks and QC reports for chromatin accessibility studies.
High-intent search queries and answers about installing and using this skill.
To process ATAC-seq data, you need a pipeline that performs adapter trimming, alignment, Tn5 shift correction, and mitochondrial filtering on raw FASTQ files to call peaks on nucleosome-free fragments, yielding high-confidence accessible chromatin regions.
To ensure ATAC-seq peak calling meets ENCODE standards, apply an automated workflow that performs Tn5 offset correction, filters mitochondrial reads, and uses IDR-based peak reproducibility assessment to guarantee high data quality and publication-ready chromatin accessibility maps.
Tn5 shift correction improves chromatin accessibility analysis by adjusting the alignment coordinates to account for the Tn5 transposase binding footprint, ensuring accurate identification of open chromatin regions during peak calling on nucleosome-free fragments.
Yes, you can use Nextflow to automate chromatin accessibility data processing, enabling scalable workflow execution across various computational environments while enforcing ENCODE standards for ATAC-seq alignment, filtering, and peak reproducibility.
Essential ATAC-seq quality metrics include TSS enrichment scores, fragment size distributions, and signal tracks, which provide comprehensive quality control for downstream interpretation of open chromatin regions and publication-ready accessibility maps.
IDR-based peak reproducibility assessment is required for ATAC-seq to evaluate peak consistency across biological replicates, ensuring that only high-confidence open chromatin regions meeting ENCODE standards are retained for downstream epigenomic analysis.
ilove323Run nf-core workflows on sequencing data to produce analysis-ready outputs and QC reports.
jaechang-hitsCall narrow or broad peaks from ChIP-seq and ATAC-seq BAM files against a control.
BIsnake2001Compute TSS enrichment, fragment-size distributions, and FRiP from BAM and peak files.
inflexa-aiStandardize ATAC-seq, ChIP-seq, and CUT&Tag analysis with peak calling and differential binding.
