Cell Ranger ARC is an advanced analytical suite designed for the Chromium Single Cell Multiome ATAC + Gene Expression sequencing. It provides in-depth analysis of gene expression and chromatin accessibility at a single cell level, uniquely linking these aspects for enhanced genomic understanding.

Overview

Getting Started

Download Center

Analysis

Tutorials

Algorithms

Advanced

Troubleshooting

Release Notes

Datasets

Loupe Browser

Cell Ranger ARC 2.1

Cell Ranger ARC

Chromium

Gene Expression

Epigenomic Profiling

Immune Profiling

Protein co-detection

Simultaneously profile gene expression and open chromatin from the same cell with Chromium Single Cell Multiome ATAC + Gene Expression. Multiply your power of discovery to characterize cell types and states, and uncover gene regulatory programs.

Unify the transcriptome and epigenome in <em>every cell</em>

Chromium X Series

Advanced system for multiomic analysis of hundreds to millions of cells.

Single Cell Multiome ATAC + Gene Expression

Combined profiling of 3' gene expression and chromatin accessibility from the same cell.

Analyze Epi Multiome ATAC + Gene Expression data with a set of free, easy-to-use pipelines for primary and secondary analyses.

A tutorial on using Cell Ranger ARC mkref to create a reference for Rattus norvegicus

Custom Reference for Rat

Understand pipeline telemetry data collection and learn how to disable it if needed

Cell Ranger ARC Pipeline Telemetry

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

Learn more about input files required to run Cell Ranger ARC

Inputs

Generating FASTQs (mkfastq)

Specifying FASTQs

FASTQs with Illumina Software

Custom Reference (mkref)

Learn more about how to run Cell Ranger ARC

Running Pipelines

Command Line Arguments

Computing Options

Analyzing GEX + ATAC (count)

Aggregating Multiple Samples (aggr)

Custom Analysis (reanalyze)

Cell Type Annotation

Learn more about the output files generated by Cell Ranger

Outputs

Web Summary

Secondary Analysis

Feature-Barcode Matrices

Summary CSV

Per Barcode QC Metrics

ATAC Barcoded BAM

ATAC Fragments

ATAC Peaks

ATAC Peak Annotations

ATAC Transposition Counts

GEX Barcoded BAM

GEX Molecule Info (H5)

HDF5 Feature Barcode Matrix Format

Cell Type Annotations

What is Cell Ranger ARC?

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}}><div><Text as={'span'} size={'small'} weight={'medium'}>{'Starting with v2.1, anonymized telemetry data is collected and sent to 10x Genomics. '}</Text><Anchor href={'https://www.10xgenomics.com/support/software/cell-ranger-arc/2.1/tutorials/cr-arc-pipeline-telemetry'}><Text as={'span'} color={'inherit'} size={'small'} weight={'medium'}>{'Learn how to disable.'}</Text></Anchor></div><Text as={'p'} size={'small'} weight={'medium'}>The cellranger-arc mkfastq pipeline is deprecated and will be removed in a future release. Please use Illumina’s BCL Convert to generate compatible FASTQ files.</Text></Flex>

Algorithms overview

Advanced pipeline content for Cell Ranger ARC.

View the latest updates to Cell Ranger ARC.

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

Access free public Chromium data from 10x Genomics.

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