Algorithms Overview

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

Cell Ranger ATAC 2.1

Cell Ranger ATAC

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?

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

Algorithms overview

Advanced pipeline content for Cell Ranger ATAC.

View the 2.1 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.