HTAN Single Cell ATAC Sequencing Data Standard


This page describes the data levels, metadata attributes, and file structure for single cell ATAC (Assay for Transposase-Accessible Chromatin) sequencing.

Description of Assay

ATAC sequencing is a sequencing method that uses an engineered Tn5 transposase to target sequencing adapters into accessible regions of chromatin. This method can be used to map transcription factor binding sites, nucleosome positioning, and other accessible regions of the chromatin surface1. Single cell ATAC sequencing employs the same methodology at single cell resolution, identifying chromatin states in subpopulations of cells within a sample2,3.

Metadata Levels

The HTAN data model currently supports Level 1 and 2 scATAC-seq data:

Level Number


Example Data


Raw unaligned data

FASTQ or BCL files containing unaligned reads.


Aligned sequence data and QC information

BAM files containing aligned sequence data. QC results captured as metadata.

1. Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods. 2017 Oct;14(10):959-962. doi: 10.1038/nmeth.4396. Epub 2017 Aug 28. PMID: 28846090; PMCID: PMC5623106.

2. Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi: 10.1038/nature14590. Epub 2015 Jun 17. PMID: 26083756; PMCID: PMC4685948.

3. Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015 May 22;348(6237):910-4. doi: 10.1126/science.aab1601. Epub 2015 May 7. PMID: 25953818; PMCID: PMC4836442.