ATAC-seq Analysis

ROSALIND's ATAC-seq Analysis module is a cloud-based discovery platform designed to make genome-wide chromatin accessibility analysis accessible to scientists of every skill level — no programming, bioinformatics, or biostatistics expertise required. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a faster and more sensitive method for assessing the epigenome compared to DNase, MNase, or FAIRE-Seq, and is widely used for nucleosome mapping, transcription factor binding site identification, DNA methylation mapping, enhancer usage studies during development, cell differentiation lineage mapping, and characterising chromatin accessibility landscapes in human cancers and other diseases.

ROSALIND connects researchers from experiment design through quality control, peak overlap analysis, differential binding, and pathway exploration in a real-time collaborative environment. By accepting raw FASTQ files as well as processed counts data, the platform delivers same-day results through an interactive, visually rich experience built to save time and accelerate discovery.

Why Study Chromatin Accessibility with ATAC-Seq

• Assess genome-wide chromatin accessibility faster and more sensitively than DNase, MNase, or FAIRE-Seq
• Perform nucleosome mapping experiments and transcription factor binding site identification
• Map DNA methylation sites using adapted ATAC-seq approaches
• Study evolutionary divergence of enhancer usage during development
• Uncover lineage-specific enhancer maps during cell differentiation
• Define genome-wide chromatin accessibility landscapes in human cancers and other diseases
• Identify cell-specific binding sites and transcription factors using computational methods

Analysis and Discovery Capabilities

• Analyze ATAC-seq data directly from raw FASTQ files
• Record experiment design and custom biological attributes
• Import NCBI Short Read Archive public data with full support for NCBI BioProject and BioSample metadata models
• Capture metadata with NCBI BioSample attributes and custom sample descriptors
• Perform covariate and batch corrections within differential comparisons
• Set up comparisons using biological attributes to minimise differential accessibility errors
• Create and customise gene filters to adjust fold-change and p-value cut-off parameters
• Explore peak overlaps to visualise open chromatin regions across the genome and multiple comparison groups
• Investigate differential accessibility of proximal promoter regions with heatmaps, volcano plots, MA plots, bar graphs, and box plots
• Explore top pathways, gene ontology diseases, and drug interaction knowledge bases interactively
• Download publication-ready figures and plots
• Conduct multi-omic analyses across experiment and assay types including ATAC-seq, ChIP-seq, and RNA-seq
• Real-time collaboration and results sharing across global teams

Five Steps to ATAC-Seq Data Analysis on ROSALIND

1. Experiment Design: Create a new experiment through a guided setup that records biological objectives, sample attributes, and analysis parameters. ROSALIND supports NCBI BioProject and BioSample models for metadata assignment, and allows custom attributes to describe biological behaviours. The platform accepts raw FASTQ files and runs an advanced pipeline including intelligent quality control, automatic contamination detection, identification of chromatin accessible regions, and deep pathway interpretation. Library preparation kit selection is supported, with the pipeline automatically calibrating for kit-specific characteristics such as unique molecular identifiers (UMIs) and adapters.
2. Quality Control: ROSALIND's Quality Control Intelligence evaluates key metrics including Q30 scores, alignment rates, duplicate rates, number of open regions detected, sample correlation, fraction of reads in peaks, genomic regions, and TSS plots. For Illumina sequencers, Q30 values should exceed 85% with alignment rates over 80%; duplicate rates should be below 25% with fewer than 10% of reads trimmed. Non-aligning reads are automatically evaluated for contamination. Researchers can flag and remove outlier samples before proceeding to the discovery phase.
3. Unlocking Results: After quality control review, researchers unlock the experiment using Analysis Units (AU), generally calculated at 1 AU per single-sample FASTQ file for ATAC-seq experiments. Account balances and options to acquire additional AU are accessible directly from the unlock screen.
4. Analysis and Discovery: ROSALIND provides a comprehensive dashboard for differential chromatin opening, moving beyond static CSV outputs. Default filters apply a fold change of +/- 1.5 with a p-Adjust below 0.05, with further automatic adjustments available. Researchers can create unlimited custom filters and adjust colour palettes, gene lists, and signatures via on-screen controls. New comparisons and meta-analyses — including cross-experiment and multi-omic analyses — can be added at any time using BioProject attributes, with results available within minutes.
5. Collaboration and Data Sharing: ROSALIND Spaces provides virtual data rooms where scientists and collaborators worldwide can interactively explore shared experiments in real time, similar to working with Google Docs. All participants access a consistent version of the data without transferring large files. Spaces support adding experiments, exploring pathways, changing cut-offs, adding meta-analyses, and creating new comparisons, with real-time activity feeds and historical reports.

Platform Highlights

• Designed for Scientists: Focused on biology and science without requiring bioinformatics, programming, or biostatistics knowledge
• Powerful Analysis: Supports contamination detection, covariate correction, batch correction, and multi-omic analyses
• Ease of Use: Clean, intuitive, and immersive user interface enabling rapid onboarding with minimal training
• Rich Data Visualisation: High-quality, interactive, publication-ready diagrams and plots
• Trusted Built-in Pipelines: Industry-standard, widely published bioinformatics tools tuned within ROSALIND's pipelines
• Flexible Data Input: Start from raw FASTQ files or processed counts data (raw or normalised)
• Security and Encryption: All communications and data are secured and encrypted

ROSALIND is available to pharma, biotech, and academic researchers through Enterprise, Professional, and Academic subscription tiers, as well as specialised licences for service providers, contract research organisations (CROs), and academic core labs. The platform integrates with NCBI public data repositories and supports a broad library of sample and library preparation kits, making it a flexible and scalable solution for epigenetics research teams.