ATAC-Seq is a next-generation sequencing (NGS) application that identifies open chromatin regions. Open chromatin refers to areas of DNA that are not protected by nucleosomes or other proteins, and often accompany sites of transcription factor binding, enhancers, and active promoters and are associated with gene activation. ATAC-Seq improves the sensitivity and input requirements of historical methods for identifying open chromatin including DNAseI Hypersensitivy Assays and FAIRE-Seq, and can be used with single cells methods. Omni-ATAC is a modified ATAC procedure that reduces mitochondrial background reads and provides consistent results with 50,000 cells.

General Workflow

ATAC-Seq utilizes a Tn5 transposase enzyme to insert sequencing adapters directly into accessible areas of double stranded DNA. Cells are first washed, then permeabilized with digitonin to allow for transposase diffusion. During incubation with Tn5, NGS platform adapters are tagged to DNA within accessible regions. The DNA is purified, and PCR extension and amplification is performed to create an NGS library.

Data Analysis

SciDAP is a no-code bioinformatics platform that enables biologists to analyze NGS-based data without a bioinformatician. It has built-in pipelines based on open-source workflows to analyze bulk data from ATAC-Seq libraries. SciDAP starts from the FASTQ files provided by most DNA core facilities and commercial service providers. Starting from raw data allows SciDAP to ensure that all experiments have been processed in the same way and simplifies the deposition of data to GEO upon publication. The data can be uploaded from the end-users’ computer, downloaded directly from an FTP server of the core facility by providing a URL, or from GEO by providing SRA accession number.

Steps in the SciDAP ATAC-Seq workflow


Start with FASTQ files

Using local files or public data accessions
ATAC fastq or SRR

Read Mapping

Map reads to reference genome, and create tracks for viewing data on IGV browser
ATAC read alignment with bowtie and peak calling with MACS2

Quality Control

Plot read and mapping statistics
ATAC QC: TSS enrichment, saturation

Browse Mapped Reads using IGV Plugin

Create coverage tracks for IGV browser
Bigwig ATAC coverage and peaks on IGV browser

Call Peaks

Peak calling with MACS2
MACS2 ATAC peaks

Binding Analysis

Differential binding analysis with diffbind, MANorm, or Thor
DiffBind analysis, volcano plots, heatmaps, PCA for ATAC

Motif Analysis with HOMER

Known or de novo motif analysis with HOMER
Motif analysis with HOMER based on various backgrounds

SciDAP is so easy to use and saves so much time, now biologists can produce publication-ready results in hours not months.