UF Health Cancer Center Bioinformatics Hub
Analysis of Omics Data by Assay
ATAC-seq

ATAC-seq

Primary Recommendation: nf-core/atacseq + atacreportR

For ATAC-seq projects, we recommend using nf-core/atacseq for initial processing followed by our atacreportR application for differential accessibility analysis and comprehensive reporting.

Workflow Overview:

  1. Raw data processing → Run nf-core/atacseq on HiperGator using SLURM configuration
  2. Differential analysis & reporting → Use atacreportR to generate comprehensive differential accessibility reports
  3. Interactive exploration → Review results through atacreportR’s downloadable reports

Important Access Notes:

  • atacreportR is a private application accessible only on the UF network
  • Contact our team for access to the required HiperGator data location to run the application
  • VPN connection required for off-campus access

Alternative R-based Analysis

For users preferring traditional R workflows, we recommend:

Best Practices & Considerations

Experimental Design:

  • Plan for adequate biological replicates (minimum 3 per condition)
  • Include appropriate input/background controls
  • Consider cell type purity and sample quality

Data Quality:

  • Evaluate fragment size distribution and TSS enrichment from nf-core/atacseq output
  • Check for proper peak calling and reproducibility between replicates
  • Assess library complexity and duplication rates

Analysis Strategy:

  • Define appropriate peak calling parameters for your cell type
  • Consider motif enrichment analysis for biological interpretation
  • Plan integration with RNA-seq data when available

Computational Resources:

  • Use HiperGator’s SLURM scheduler for nf-core/atacseq processing
  • Allocate sufficient memory for peak calling (depends on genome size)
  • Plan storage for large BAM files and peak call outputs

Getting Started

Submit a support request to discuss your ATAC-seq project design, analysis needs, and to obtain access to atacreportR.