Cell Ranger ATAC

What is Cell Ranger ATAC?

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.

Download Cell Ranger ATAC Get Started with Cell Ranger ATAC

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.

Analysis

Inputs

Learn more about input files required to run Cell Ranger ATAC

Running Pipelines

Learn more about how to run Cell Ranger ATAC

Outputs

Learn more about the output files generated by Cell Ranger ATAC

Algorithms overview

Overview of Cell Ranger ATAC algorithms.

Advanced

Advanced pipeline content for Cell Ranger ATAC.

Troubleshooting

Learn how to troubleshoot common errors.

Release Notes

View the latest updates to Cell Ranger ATAC.

Q&A

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

Glossary

View terms and definitions relevant to Epi ATAC.

Datasets

Access free public Chromium data from 10x Genomics.

Loupe Browser

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