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ATAC-sequencing Analysis

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) provides a rapid, sensitive, genome-wide view of chromatin accessibility—revealing the regulatory landscape of a cell or tissue with relatively low input material. As the technique becomes increasingly routine, ATAC-seq has become a powerful and accessible tool for studying gene regulation, transcription factor binding, and chromatin remodelling across a wide range of biological systems.

 

For many groups, the challenge lies not in generating the data, but in processing and interpreting it correctly. ATAC-seq carries specific analytical considerations—including mitochondrial read filtering, nucleosome-based fragment size assessment, and careful normalisation—that require expert handling to produce reliable, publication-ready results. At Porter-Turnbull Genomics Consultancy, we ensure your chromatin accessibility data is analysed rigorously and interpreted in its full biological context.

How Projects Run

All ATAC-seq projects are scoped individually to ensure the analysis strategy is appropriate for the experimental system, sample type, and biological question.

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  • Initial project planning meeting

An online discussion to review experimental design, controls, sequencing depth, and analytical objectives before any processing begins.​

  • Transparent, reproducible analysis

All analyses are performed using documented, reproducible workflows, with clear communication around key decisions such as mitochondrial filtering thresholds, peak calling parameters, and normalisation strategy.​

  • Results review and next steps

A final meeting to walk through results, visualisations, and biological interpretation, with guidance on follow-up analyses, validation, or publication preparation.

Raw Data Processing

Starting from £40 per sample

  • Processing of paired-end ATAC-seq data using reproducible pipelines built with Conda, Python, and Snakemake

  • Alignment to the appropriate reference genome using Bowtie2

  • Comprehensive quality control including FASTQC summaries, alignment metrics, mitochondrial read assessment, and fragment size distribution

  • Removal of duplicates, mitochondrial reads, and ENCODE blacklist regions

  • Nucleosome-free region (NFR) and mono-nucleosomal fragment separation

  • Peak calling using MACS2 optimised for ATAC-seq data

  • IDR analysis to identify reproducible peaks across biological replicates

  • Generation of normalised BigWig files for interactive genome browser visualisation

  • Fixed software versions and fully documented parameters to ensure reproducibility

  • Standard pipelines that can be customised to assay type or experimental design

Basic Differential Gene Expression Analysis

Processing + basic analysis from £70 per sample

Includes everything in Raw data processing, plus:

  • Annotation of accessible peaks to genomic features (promoters, enhancers, intronic and intergenic regions)

  • TSS enrichment scoring and library quality assessment

  • Signal heatmaps and average profiles at transcription start sites and peak centres

  • Genome browser snapshots for representative loci

  • Comparative peak overlap analysis between conditions

  • Clear, annotated results tables summarising accessibility statistics

  • Results meeting to discuss findings, interpretation, and biological relevance

Advanced Analysis

Processing + basic + advanced analysis from £110 per sample

Includes everything in Basic accessibility analysis, plus:

  • Differential chromatin accessibility analysis between conditions using DESeq2

  • Transcription factor motif enrichment analysis using HOMER and/or MEME-suite

  • ChromVAR-based inference of transcription factor activity across samples

  • Integration with RNA-seq, ChIP-seq, or other omics data where available

  • Nucleosome positioning and chromatin state analysis

  • Pathway or gene-set enrichment analysis based on accessibility-associated genes

  • Iterative development of publication-ready figures and supplementary materials

  • Support with biological interpretation and results framing

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Packages are available for complete project support, from raw data processing through to publication-ready results.

All prices are indicative and may vary depending on experimental design, dataset size, species, and analytical scope. Academic and multi-sample project discounts are available.

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