tar.gz compression

Download for Linux 64-bit (tar.gz)

The 20,000 total cell limit has been removed from cellranger-atac pipelines, enabling the analysis of large datasets

Strand information is now included in the fragments.tsv file for easier downstream analysis

The --nosecondary parameter is now enabled for count and aggr pipelines

Cell Ranger ATAC 2.2.0 highlights

To set up and run Cell Ranger ATAC on Linux, please follow the steps below, or skip download and installation and get started with 10x Cloud Analysis:

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References

Cell Ranger ATAC

Download Cell Ranger ATAC

Added a batch correction algorithm to `cellranger-atac aggr`

Cell Ranger ATAC 2.1.0 highlights

Cell Ranger ATAC and Loupe Browser are software applications for analyzing and visualizing Epi ATAC (formerly Single Cell ATAC) data produced by the 10x Genomics Chromium platform.

Overview

Getting Started

Download Center

Analysis

Algorithms

Advanced

Troubleshooting

Release Notes

Glossary

Datasets

Loupe Browser

Learn more about input files required to run Cell Ranger ATAC

Inputs

Generating FASTQs (mkfastq)

Specifying Input FASTQs

Demultiplexing with Illumina Software

Creating a Reference Package (mkref)

Learn more about how to run Cell Ranger ATAC

Running Pipelines

Command Line Arguments

Single Library Analysis (count)

Aggregate Multiple GEM Wells (aggr)

Customized Secondary Analysis (reanalyze)

Learn more about the output files generated by Cell Ranger ATAC

Outputs

Web Summary

Secondary Analysis Results

Feature-Barcode Matrices

HDF5

Per Barcode QC, ATAC Signal, and Cell Calling

Barcoded BAMs

Fragments File

Peaks File

Summary Metrics

Peak Annotations

What is Cell Ranger ATAC?

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}}><div><Text as={'span'} size={'small'} weight={'medium'}>{'The cellranger-atac mkfastq pipeline is deprecated and will be removed in a future release. Please use Illumina’s BCL Convert to generate Cell Ranger-compatible FASTQ files.'}</Text></div></Flex>

We provide resources from protocols, user guides, and free-to-use analysis tools

Algorithms overview

Advanced pipeline content for Cell Ranger ATAC.

View the latest updates to Cell Ranger ATAC.

Browse Q&As from the 10x Genomics support team.

View terms and definitions relevant to Epi ATAC.

Access free public Chromium data from 10x Genomics.

Loupe Browser is a desktop application that allows you to interactively visualize data.

Previous Versions

Cell Ranger ATAC 2.2.0 (Apr 30, 2025)

Cell Ranger ATAC 2.2.0 highlights

Cell Ranger ATAC 2.1.0 (Apr 4, 2022)

Cell Ranger ATAC 2.1.0 highlights