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

Downloads & Installation

Analysis

Tutorials

Algorithms

Advanced

Troubleshooting

Release Notes

Datasets

Loupe Browser

Cell Ranger ARC

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

Custom Reference for Rat

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

Analyzing GEX + ATAC (count)

Aggregating Multiple Samples (aggr)

Custom Analysis (reanalyze)

Learn more about the output files generated by Cell Ranger

Outputs

Web Summary

ATAC + Gene Expression Analysis

Feature-Barcode Matrices

Per Barcode Metrics

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

What is Cell Ranger ARC?

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

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.