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Cell Ranger ARC

Cell Ranger ARC

software-intro
What is 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.

Download Cell Ranger ARCGet Started with Cell Ranger ARC
Starting with v2.1, anonymized telemetry data is collected and sent to 10x Genomics. Learn how to disable.

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.

Analysis

Inputs

Learn more about input files required to run Cell Ranger ARC

Running Pipelines

Learn more about how to run Cell Ranger ARC

Outputs

Learn more about the output files generated by Cell Ranger

Tutorials

Custom Reference for Rat
A tutorial on using Cell Ranger ARC mkref to create a reference for Rattus norvegicus
Cell Ranger ARC Pipeline Telemetry
Understand pipeline telemetry data collection and learn how to disable it if needed

Algorithms overview

Overview of Cell Ranger ARC algorithms.

Advanced

Advanced pipeline content for Cell Ranger ARC.

Troubleshooting

Learn how to troubleshoot common errors.

Release Notes

View the latest updates to Cell Ranger ARC.

Q&A

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

Datasets

Access free public Chromium data from 10x Genomics.

Loupe Browser

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