tar.gz compression

Download for Linux 64-bit (tar.gz)

New feature: wavelet-based peak caller to improve detection of cluster-specific peaks

Improvements to duplicate marking algorithm

Improvements to computational performance: ~4x faster, 0.5x disk requirements

Cell Ranger ARC 2.0.2 highlights

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

<Grid gap={'2rem'}><Anchor href={'/support/software/cell-ranger-arc/downloads/ref-build-steps'} style={{display: 'flex', gap: '9px', alignItems:'center', padding: '.5rem 0'}} > <Text as={'p'} color={'inherit'} size={'small'} weight={'medium'}> View steps to build references </Text> <Icon source={'nav-right'} color={'inherit'} size={'9px'} yPos={'1px'}/> </Anchor><DownloadLinkList softwareSlug={'cell-ranger-arc'} eula={false} downloadLinks={[ {subtitle:'Human reference (GRCh38) - 2020-A',fileSizeKB:14000000,md5Sum:'2f12f6016197869e21e5559827002716',title: 'Download Human Reference', summary:['Human reference (GRCh38) dataset required for Cell Ranger ARC.'], batch: true, url: 'https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-GRCh38-2020-A-2.0.0.tar.gz'},{subtitle:'Mouse reference (mm10) - 2020-A',fileSizeKB:13000000, md5Sum:'a2c1cc9b8dff2a2ef36971d7c31c8304', title: 'Download Mouse Reference', summary:['Mouse reference (mm10) dataset required for Cell Ranger ARC.'], batch: true, url: 'https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz'} ]} /></Grid>

References

Cell Ranger ARC

Download Cell Ranger ARC

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

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.

Previous Versions

Cell Ranger ARC 2.0.2 (Aug 18, 2022)

Cell Ranger ARC 2.0.2 highlights