
<LinkableSection id={"3p-library"} title={"Single Cell Gene Expression"}>

<LinkableSection id={"3p-library-v4"} nested={true} title={"v4"} >

| Library Combination                      | CR 8.0    | CR 7.2 and lower |
| ---------------------------------------- | --------- | ---------------- |
| 3’ Gene Expression v4                    | <Check /> | -                |
| 3’ Gene Expression v4 + Antibody Capture | <Check /> | -                |

Chromium GEM-X Single Cell Gene Expression v4 chemistry does **not** support the following library types:

- 3' Gene Expression v4 + CellPlex (not supported)
- 3' Gene Expression v4 + CRISPR Guide Capture (not supported)

Accordingly, Cell Ranger v8.0 cannot process these libraries.
</LinkableSection>

<LinkableSection id={"3p-library-v3"} nested={true} title={"v3 and lower"} >
| Library Combination | CR 8.0 | CR 7.2 | CR 7.1 | CR 7.0 | CR 6.1| CR 6.0 | CR 5.0 | CR 4.0 | CR 3.1 | CR 3.0 | CR 2.2 |
| --------------------------------------------------------| --------- | --------- | --------- | --------- | --------- | --------- | --------- | --------- | --------- | --------- | --------- |
| 3’ Gene Expression v2 | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> |
| 3’ Gene Expression v3 | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | - |
| 3’ Gene Expression v3 + Cell Surface Protein | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | - |
| 3’ Gene Expression v3 + CRISPR Screening Expression | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | - |
| 3’ Cell Surface Protein only | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | - | - |
| 3’ Targeted Gene Expression | - | - | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | - | - | - |
| 3’ Cell Multiplexing | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | - | - | - | - | - |
| 3’ LT (Low Throughput) | - | <Check /> | <Check /> | <Check /> | <Check /> | - | - | - | - | - | - |
| 3’ HT (High Throughput) | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | - | - | - | - | - | - |

</LinkableSection>

<LinkableSection id={"5p-library"} title={"Immune Profiling"}>

<LinkableSection id={"5p-library-v3"} nested={true} title={"v3"} >

| Library Combination                                   | CR 8.0    | CR 7.2 and lower |
| ----------------------------------------------------- | --------- | ---------------- |
| 5’ Gene Expression v3                                 | <Check /> | -                |
| 5’ Gene Expression v3 + V(D)J                         | <Check /> | -                |
| 5’ Gene Expression v3 + Cell Surface Protein          | <Check /> | -                |
| 5’ Gene Expression v3 + Cell Surface Protein + V(D)J  | <Check /> | -                |
| 5’ Gene Expression v3 + Cell Surface Protein + CRISPR | <Check /> | -                |
| 5’ Gene Expression v3 + CRISPR                        | <Check /> | -                |
| 5’ Gene Expression v3 + V(D)J + CRISPR                | <Check /> | -                |
| 5’ Gene Expression v3 + CSP + V(D)J + CRISPR          | <Check /> | -                |

Chromium GEM-X Single Cell Immune Profiling v3 chemistry does **not** support the following library types:

- 5' Gene Expression v3 + V(D)J + Antigen Capture (not supported)

However, Cell Ranger v8.0 can process 5' Gene Expression + V(D)J libraries + Antigen Capture generated using Next GEM v2 chemistry (see below).

</LinkableSection>
</LinkableSection>

<LinkableSection id={"5p-library-v2"} nested={true} title={"v2 and lower"} >

| Library Combination                                                 | CR 8.0    | CR 7.2    | CR 7.1    | CR 7.0    | CR 6.1    | CR 6.0    | CR 5.0    | CR 4.0    | CR 3.1    | CR 3.0    | CR 2.2    |
| ------------------------------------------------------------------- | --------- | --------- | --------- | --------- | --------- | --------- | --------- | --------- | --------- | --------- | --------- |
| 5’ Gene Expression                                                  | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> |
| 5’ V(D)J                                                            | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> |
| 5’ Gene Expression + V(D)J                                          | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> |
| 5’ Gene Expression + Cell Surface Protein                           | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | -         |
| 5’ Gene Expression + Cell Surface Protein + V(D)J                   | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | -         |
| V(D) J + Cell Surface Protein                                       | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | -         |
| 5’ Cell Surface Protein only                                        | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | -         | -         |
| 5’ Targeted Gene Expression                                         | -         | -         | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | <Check /> | -         | -         | -         |
| 5’ HT (High Throughput)                                             | <Check /> | <Check /> | <Check /> | <Check /> | -         | -         | -         | -         | -         | -         | -         |
| 5’ Gene Expression + CRISPR                                         | <Check /> | <Check /> | <Check /> | -         | -         | -         | -         | -         | -         | -         |
| 5’ Gene Expression + CRISPR + Cell Surface Protein                  | <Check /> | <Check /> | <Check /> | -         | -         | -         | -         | -         | -         | -         |
| 5’ Gene Expression + CRISPR + V(D)J                                 | <Check /> | <Check /> | <Check /> | -         | -         | -         | -         | -         | -         | -         |
| 5’ Gene Expression + Antigen Capture + V(D)J ± Cell Surface Protein | <Check /> | <Check /> | -         | -         | -         | -         | -         | -         | -         | -         |

</LinkableSection>

<LinkableSection id={"frp-library"} title={"Fixed RNA Profiling"}>

| Library Combination                                        | CR 8.0    | CR 7.2    | CR 7.1    | CR 7.0    |
| ---------------------------------------------------------- | --------- | --------- | --------- | --------- |
| Gene expression (singleplex or multiplex)                  | <Check /> | <Check /> | <Check /> | <Check /> |
| Gene expression + Antibody Capture (singleplex)            | <Check /> | <Check /> | <Check /> | <Check /> |
| Single cell FFPE Gene Expression (singleplex or multiplex) | <Check /> | <Check /> | <Check /> | -         |
| Gene expression + Antibody Capture (multiplex)             | <Check /> | <Check /> | -         | -         |

</LinkableSection>
</LinkableSection>


Single Cell Gene Expression

v3 and lower

Immune Profiling

v2 and lower

Fixed RNA Profiling

Supported Libraries

Libraries Supported by Cell Ranger

Resources

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

Download Center

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

View all tutorials

Learn more about input files required to run Cell Ranger

Inputs

Generating FASTQs

Specifying FASTQs

Custom Reference with mkref

Custom V(D)J Reference

Running Pipelines

Choosing a pipeline

GEX (count)

Antibody/CRISPR (count)

3' Cell Multiplexing (multi)

VDJ-T/B only (vdj)

VDJ + GEX + FB/BEAM (multi)

Fixed RNA Profiling (multi)

Aggregate Multiple Samples (aggr)

Custom Analysis (reanalyze)

Learn more about the output files generated by Cell Ranger

Outputs

Web Summary

Metrics

Feature-Barcode Matrices

Molecule Info (H5)

Secondary Analysis

Results of aggr

Gene Expression

Antibody Capture

CRISPR Guide Capture

Cell Multiplexing

VDJ-T/B

VDJ + GEX + BEAM

What is Cell Ranger?

<Text as={'p'} size={'small'} weight={'medium'}>Cell Ranger v8.0 introduces support for the analysis of GEM-X libraries. <br></br>Cell Ranger v7.2 is the last version to support the analysis of LT (low throughput) libraries.</Text>

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.

Library Combination	CR 8.0	CR 7.2 and lower
3’ Gene Expression v4		-
3’ Gene Expression v4 + Antibody Capture		-

Library Combination	CR 8.0	CR 7.2	CR 6.0	CR 5.0	CR 4.0	CR 3.1	CR 3.0	CR 2.2
3’ Gene Expression v2
3’ Gene Expression v3								-
3’ Gene Expression v3 + Cell Surface Protein								-
3’ Gene Expression v3 + CRISPR Screening Expression								-
3’ Cell Surface Protein only							-	-
3’ Targeted Gene Expression	-	-				-	-	-
3’ Cell Multiplexing				-	-	-	-	-
3’ LT (Low Throughput)	-		-	-	-	-	-	-
3’ HT (High Throughput)			-	-	-	-	-	-

Library Combination	CR 8.0	CR 7.2 and lower
5’ Gene Expression v3		-
5’ Gene Expression v3 + V(D)J		-
5’ Gene Expression v3 + Cell Surface Protein		-
5’ Gene Expression v3 + Cell Surface Protein + V(D)J		-
5’ Gene Expression v3 + Cell Surface Protein + CRISPR		-
5’ Gene Expression v3 + CRISPR		-
5’ Gene Expression v3 + V(D)J + CRISPR		-
5’ Gene Expression v3 + CSP + V(D)J + CRISPR		-

Library Combination	CR 8.0	CR 7.2	CR 7.1	CR 7.0	CR 6.1	CR 6.0	CR 5.0	CR 4.0	CR 3.1	CR 3.0	CR 2.2
5’ Gene Expression
5’ V(D)J
5’ Gene Expression + V(D)J
5’ Gene Expression + Cell Surface Protein											-
5’ Gene Expression + Cell Surface Protein + V(D)J											-
V(D) J + Cell Surface Protein											-
5’ Cell Surface Protein only										-	-
5’ Targeted Gene Expression	-	-							-	-	-
5’ HT (High Throughput)					-	-	-	-	-	-	-
5’ Gene Expression + CRISPR				-	-	-	-	-	-	-
5’ Gene Expression + CRISPR + Cell Surface Protein				-	-	-	-	-	-	-
5’ Gene Expression + CRISPR + V(D)J				-	-	-	-	-	-	-
5’ Gene Expression + Antigen Capture + V(D)J ± Cell Surface Protein			-	-	-	-	-	-	-	-

Library Combination	CR 7.1	CR 7.0
Gene expression (singleplex or multiplex)
Gene expression + Antibody Capture (singleplex)
Single cell FFPE Gene Expression (singleplex or multiplex)		-
Gene expression + Antibody Capture (multiplex)	-	-