A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.

Overview

Getting Started

Supported Libraries

Download Center

Cloud Analysis

Cell Ranger Commands

Analysis

Tutorials

Algorithms

Advanced

Troubleshooting

Miscellaneous

Release Notes

Glossary

Datasets

Loupe Browser

Cell Ranger

Installation

Get Started with Cell Ranger

Convert BCL to FASTQ with Cell Ranger mkfastq

mkfastq

Cell Ranger mkfastq

Analyze Gene Expression and Feature Barcode data with Cell Ranger count

count

Cell Ranger count

aggr

Cell Ranger aggr

Rerun secondary analysis for a completed cellranger count or aggr run with different parameters

reanalyze

Cell Ranger reanalyze

Build a custom reference using Cell Ranger mkref

mkref

Cell Ranger mkref

Analyze cell multiplexing data with Cell Ranger multi

multi

Cell Ranger multi for 3' Cell Multiplexing

Analyze V(D)J and 5' GEX with Cell Ranger multi

multi for V(D)J

Cell Ranger multi for Immune Profiling

Analyze your GEX + VDJ + B cell Antigen Capture libraries with Cell Ranger multi

Cell Ranger multi for BEAM-Ab

Analyze your GEX + VDJ + T cell Antigen Capture libraries with Cell Ranger multi

Cell Ranger multi for BEAM-T

Analyze V(D)J libraries with Cell Ranger vdj

Cell Ranger vdj

Capturing Neutrophils in 10x Single Cell Gene Expression Data

Capturing neutrophils

Capturing Neutrophils

Analyze scRNA-Seq Data From a Publication Using 10x Software

Data analysis

Example Data Analysis

Analysis and visualization of data in the tumor microenvironment application note using the Loupe and Loupe V(D)J Browsers

Characterize tumor cells

Tumor Microenvironment Data Analysis and Visualization

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

Cell Ranger Pipeline Telemetry

View all tutorials

Learn more about input files required to run Cell Ranger

Inputs

List of Inputs

Generating FASTQs

Specifying FASTQs

A CSV file used to indicate the input FASTQ files for libraries in a Feature Barcode experiment.

Libraries CSV

A CSV file used to indicate the molecule structure and unique Feature Barcode sequence of each feature present in the experiment.

Feature Reference CSV

A CSV files that specifies parameters required to run cellranger multi

Multi Config CSV

Custom Reference with mkref

Custom V(D)J Reference

Running Pipelines

Choosing a pipeline

multi (3'/5'/Flex)

count (GEX + Antibody/CRISPR)

vdj (VDJ-T/B only)

Data Integration Workflows

Cell Annotation (annotate)

Custom Analysis (reanalyze)

Learn more about the output files generated by Cell Ranger

Outputs

Outputs by pipeline

Web Summary

Metrics

Feature-Barcode Matrices

Molecule Info (H5)

Secondary Analysis

Results of aggr

Gene Expression

Antibody Capture

CRISPR Guide Capture

VDJ-T/B

3'/5' Singleplex (GEX + VDJ + FB)

3'/5' Sample Multiplexing (GEX + VDJ + FB)

Flex (Singleplex & Multiplex)

What is Cell Ranger?

<Flex style={{
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}}><div><Text as={'span'} size={'small'} weight={'medium'}>{'Starting with v9.0, anonymized telemetry data is collected and sent to 10x Genomics. '}</Text><Anchor href={'https://10xgen.com/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'}>Fixed RNA Profiling has been renamed Flex. All future updates, documentation, and support will reference Flex.</Text><Text as={'p'} size={'small'} weight={'medium'}>The cellranger mkfastq pipeline is deprecated and will be removed in a future release. Please use Illumina’s BCL Convert to generate Cell Ranger-compatible FASTQ files.</Text></Flex>

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

Algorithms overview

Advanced pipeline content for Cell Ranger.

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

View terms and definitions relevant to Single Cell products.

Access free public Chromium data from 10x Genomics.

A collection of introductions, tutorials, and blogs for data analysis beyond software.

Analysis Guides

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