Nucleosome Positioning - Usage Guide

Nucleosome Positioning - Usage Guide

Overview

Extract nucleosome positions from ATAC-seq fragment size patterns using ATACseqQC or NucleoATAC to understand chromatin structure at promoters and regulatory regions.

Prerequisites

BiocManager::install(c('ATACseqQC', 'TxDb.Hsapiens.UCSC.hg38.knownGene'))

pip install nucleoatac

Quick Start

Tell your AI agent what you want to do:

• "Analyze nucleosome positioning from my ATAC-seq data"
• "Generate fragment size distribution to check nucleosome periodicity"

Example Prompts

Fragment Size Analysis

"Plot the fragment size distribution from my ATAC-seq BAM to visualize nucleosome patterns"

Nucleosome Calling

"Call nucleosome positions from my ATAC-seq data using NucleoATAC"

TSS Nucleosome Patterns

"Analyze nucleosome positioning around TSS to visualize NFR and +1/-1 nucleosomes"

NFR Analysis

"Extract nucleosome-free region reads and analyze coverage at promoters"

What the Agent Will Do

1. Calculate fragment size distribution to verify nucleosome periodicity
2. Separate reads by fragment size (NFR, mono-, di-, tri-nucleosomal)
3. Call nucleosome positions using NucleoATAC or ATACseqQC
4. Generate nucleosome occupancy signal tracks
5. Visualize nucleosome patterns around TSS

Fragment Size Interpretation

Nucleosome Pattern Interpretation

Tips

• Paired-end data is required for accurate fragment sizing
• Use properly deduplicated BAM files
• Filter for high-quality fragments (MAPQ > 30)
• High mitochondrial contamination can skew fragment distributions
• NucleoATAC provides base-pair resolution nucleosome positions
• ATACseqQC is useful for V-plots around TSS showing nucleosome phasing