Instructions for building the 10x Genomics Public Reference are documented separately.
<CTAButton href="/support/software/cell-ranger/downloads/cr-ref-build-steps" label="Build Steps" size={{height: "30px", width: "250px"}} icon="external-link" target="\_blank" mode="light" /> 


<LinkableSection id={"transcriptome"} title={"Transcriptome reference"}>

<LinkableSection id={"2024-a"} nested={true} title={"2024-A (Mar 13, 2024)"}>
</LinkableSection>

2024-A reference packages are **not** backward compatible with Cell Ranger v5.0.1 and prior.

* Human GRCh38 (GENCODE v44/Ensembl110 annotations)
* Mouse GRCm39 (GENCODE vM33/Ensembl110 annotations)
* Human and mouse GRCh38 and GRCm39

#### Update notes:

* Human transcriptome annotations have been updated from GENCODE v32 to GENCODE v44.
* Mouse transcriptome annotations have been updated from vM23 to vM33.
* Readthrough annotations have been improved, and erroneous systematic gene names have been removed.
* Polymorphic pseudogenes were included by adding `protein_coding_LoF` to the list of accepted biotypes.
* Pseudoautosomal regions (PAR) on the Y chromosome have been masked and the pseudoautosomal genes on the Y chromosome have been removed from the GTF. The corresponding genes on the X chromosome are still present in the GTF and will have associated counts.
* Summary of changes is shown in the table:

| |Human | Mouse |
|------------------------|------|-------|
| Number of new gene IDs | 2339 | 1746 |
| Number of genes removed | 301 | 335 |
| Number of gene names changed | 12913 | 1905 |
| Number of gene IDs changed (based on gene name) | 69 | 56 |

* List of affected [human](https://cdn.10xgenomics.com/raw/upload/v1709938037/software-support/Cell%20Ranger/2024-A_Reference/2020-2024-human-detailed-changes.csv) and [mouse](https://cdn.10xgenomics.com/raw/upload/v1709340128/software-support/Cell%20Ranger/2024-A_Reference/2020-2024-mouse-detailed-changes.csv) genes are available for download. 

<LinkableSection id={"2020-a"} nested={true} title={"2020-A (Jul 7, 2020)"}>

2020-A reference packages are backward compatible with Cell Ranger v3.1.0 and prior.

Human GRCh38 (GENCODE v32/Ensembl98)<CTAButton href="https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz" label="Download" size={{height: "30px", width: "150px"}} icon="external-link" target="\_blank" mode="light" /> 

Mouse mm10 (GENCODE vM23/Ensembl98)<CTAButton href="https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz" label="Download" size={{height: "30px", width: "150px"}} icon="external-link" target="\_blank" mode="light" /> 

Human and mouse GRCh38 and mm10<CTAButton href="https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-and-mm10-2020-A.tar.gz" label="Download" size={{height: "30px", width: "150px"}} icon="external-link" target="\_blank" mode="light" /> 

#### Update notes:
* Transcriptome annotations updated from Ensembl 93 to GENCODE v32 (human) and vM23 (mouse), which are equivalent to Ensembl 98.
* GRCh38 and mm10 sequences are not changed; chromosome names now follow the GENCODE/UCSC convention (e.g., chr1 and chrM) rather than the Ensembl convention (1 and MT).
* Additional filtering removes genes with unreliable annotations that often overlap more legitimate genes (see build scripts for details), resulting in improved overall sensitivity.
* Mapping rates and gene/UMI sensitivity are increased due to more comprehensive annotations and improved manual curation of genes:

<Image src={"https://cdn.10xgenomics.com/image/upload/v1690574422/software-support/Cell%20Ranger/reference_update_3.0-2020A_mapping_metrics.png"} />
 

</LinkableSection>


<LinkableSection id={"3.1.0"} nested={true} title={"3.1.0 (Jul 24, 2019)"}>

Human and mouse 3.1.0 GRCh38 and mm10
</LinkableSection>

<LinkableSection id={"3.0.0"} nested={true} title={"3.0.0 (Nov 19, 2018)"}>

Human 3.0.0 GRCh38
Human 3.0.0 hg19
Mouse 3.0.0 mm10
Human and mouse 3.0.0 hg19 and mm10
</LinkableSection>

<LinkableSection id={"2.1.0"} nested={true} title={"2.1.0 (Feb 7, 2018)"}>

Mouse mm10 (V(D)J genes included)
Human and house hg19 and mm10 (with V(D)J)
</LinkableSection>


<LinkableSection id={"1.2.0"} nested={true} title={"1.2.0 (Nov 16, 2016)"}>

Human 1.2.0 GRCh38
Human 1.2.0 hg19
Mouse 1.2.0 mm10
Human and mouse 1.2.0 hg19 and mm10
ERCC reference ercc92

</LinkableSection>
</LinkableSection>


<LinkableSection id={"vdj-ref"} title={"V(D)J reference"}>
</LinkableSection>

<LinkableSection id={"cr7-1"} nested={true} title={"CR 7.1"}></LinkableSection>

#### Human V(D)J reference GRCh38

The Human V(D)J reference has been updated to exclude the following genes:
* IGHV4-30-2
* IGKV1D-33
* IGKV1D-37
* IGKV1D-39
* IGKV2D-28

These genes have counterparts with identical V, D, J, and C gene sequences, but differ in the length of their 5' UTRs. Removing duplicates improves clonotype assignment.

<LinkableSection id={"cr7-0"} nested={true} title={"CR 7.0"}></LinkableSection>

* Added human gene IGHV3-9
* For two genes that are identical except for extra bases on the 3' end, only the longer version was retained. List of affected genes:

HUMAN:

```
IGHA1 ENST00000390547 
IGHD ENST00000390556 
IGHD1-1 ENST00000454908 
IGHD1-14 ENST00000451044 
IGHD1-20 ENST00000450276 
IGHD1-26 ENST00000390567 
IGHD1-7 ENST00000430425 
IGHD1/OR15-1A ENST00000605284 
IGHD2-15 ENST00000390578 
IGHD2-2 ENST00000390591 
IGHD2-21 ENST00000390572 
IGHD2-8 ENST00000390585 
IGHD2/OR15-2A ENST00000603077 
IGHD3-10 ENST00000390583 
IGHD3-16 ENST00000390577 
IGHD3-22 ENST00000390571 
IGHD3-3 ENST00000390590 
IGHD3-9 ENST00000390584 
IGHD3/OR15-3A ENST00000604950 
IGHD4-11 ENST00000431440 
IGHD4-17 ENST00000431870 
IGHD4-23 ENST00000437320 
IGHD4/OR15-4A ENST00000603326 
IGHD5-12 ENST00000390581 
IGHD5-18 ENST00000390575 
IGHD5-24 ENST00000390569 
IGHD5/OR15-5A ENST00000604642 
IGHD6-13 ENST00000390580 
IGHD6-19 ENST00000390574 
IGHD6-25 ENST00000452198 
IGHD6-6 ENST00000454691 
IGHD7-27 ENST00000439842 
IGHG1 ENST00000390542 
IGHG1 ENST00000390548 
IGHG1 ENST00000390549 
IGHG2 ENST00000390545 
IGHG3 ENST00000390551 
IGHG4 ENST00000390543 
IGHJ1 ENST00000390565 
IGHM ENST00000390559 
IGHV1-18 ENST00000390605 
IGHV1-2 ENST00000390594 
IGHV1-24 ENST00000390610 
IGHV1-3 ENST00000390595 
IGHV1-45 ENST00000390621 
IGHV1-46 ENST00000390622 
IGHV1-58 ENST00000390628 
IGHV1-69 ENST00000390633 
IGHV1-69-2 ENST00000615784 
IGHV2-26 ENST00000390611 
IGHV2-5 ENST00000390597 
IGHV2-70D ENST00000390634 
IGHV3-11 ENST00000390601 
IGHV3-13 ENST00000390602 
IGHV3-15 ENST00000390603 
IGHV3-16 ENST00000390604 
IGHV3-20 ENST00000390606 
IGHV3-21 ENST00000390607 
IGHV3-23 ENST00000390609 
IGHV3-30 ENST00000603660 
IGHV3-35 ENST00000390617 
IGHV3-38 ENST00000390618 
IGHV3-43 ENST00000434710 
IGHV3-48 ENST00000390624 
IGHV3-49 ENST00000390625 
IGHV3-53 ENST00000390627 
IGHV3-64 ENST00000454421 
IGHV3-66 ENST00000390632 
IGHV3-7 ENST00000390598 
IGHV3-72 ENST00000433072 
IGHV3-73 ENST00000390636 
IGHV3-74 ENST00000424969 
IGHV4-28 ENST00000390612 
IGHV4-34 ENST00000390616 
IGHV4-39 ENST00000390619 
IGHV4-4 ENST00000455737 
IGHV4-59 ENST00000390629 
IGHV4-61 ENST00000390630 
IGHV5-51 ENST00000390626 
IGHV6-1 ENST00000390593 
IGKV1-12 ENST00000480492 
IGKV1-16 ENST00000479981 
IGKV1-17 ENST00000490686 
IGKV1-27 ENST00000498435 
IGKV1-33 ENST00000473726 
IGKV1-37 ENST00000465170 
IGKV1-39 ENST00000498574 
IGKV1-5 ENST00000496168
 IGKV1-6 ENST00000464162 
IGKV1-8 ENST00000495489 
IGKV1-9 ENST00000493819 
IGKV2-24 ENST00000484817 
IGKV2-28 ENST00000482769 
IGKV2-30 ENST00000468494 
IGKV3-11 ENST00000483158 
IGKV3-15 ENST00000390252 
IGKV3-20 ENST00000492167 
IGKV3-7 ENST00000390247
IGKV3D-7 ENST00000443397 
IGKV5-2 ENST00000390244 
IGKV6-21 ENST00000390256 
IGLV1-36 ENST00000390301 
IGLV1-40 ENST00000390299 
IGLV1-44 ENST00000628287 
IGLV2-33 ENST00000390302 
IGLV3-32 ENST00000390303 
IGLV5-37 ENST00000390300 
IGLV7-43 ENST00000390298 
TRBD1 ENST00000631435 
TRBJ1-1 ENST00000634213 
TRBJ1-2 ENST00000631745 
TRBJ1-3 ENST00000633780 
TRBJ1-4 ENST00000632041 
TRBJ1-5 ENST00000634000 
TRBJ2-1 ENST00000390412 
TRBJ2-2 ENST00000390413 
TRBJ2-2P ENST00000390414 
TRBJ2-3 ENST00000390415 
TRBJ2-4 ENST00000390416 
TRBJ2-5 ENST00000390417 
TRBJ2-6 ENST00000390418 
TRBV10-1 ENST00000390364 
TRBV11-1 ENST00000390367 
TRBV11-3 ENST00000611787 
TRBV12-3 ENST00000620569 
TRBV13 ENST00000614171 
TRBV14 ENST00000617639 
TRBV15 ENST00000616518 
TRBV16 ENST00000620773 
TRBV23-1 ENST00000390396 
TRBV27 ENST00000390399 
TRBV28 ENST00000390400 
TRBV29-1 ENST00000422143 
TRBV3-1 ENST00000390387
TRBV4-2 ENST00000390392 
TRBV5-1 ENST00000390381 
TRBV5-6 ENST00000390375 
TRBV5-7 ENST00000390378 
TRBV6-1 ENST00000390353 
TRBV6-5 ENST00000390368 
TRBV7-1 ENST00000547918 
TRBV7-7 ENST00000390377 
TRGJ1 ENST00000390337

```


MOUSE:

Added missing mouse TRGV and TRGC genes

```
TRGC1 ENSMUST00000103558 TRGC2 ENSMUST00000103561 TRGC3 ENSMUST00000198163 TRGC4 ENSMUST00000179181 TRGV1 ENSMUST00000103564 TRGV3 ENSMUST00000198663 TRGV4 ENSMUST00000103554 TRGV5 ENSMUST00000199017 TRGV6 ENSMUST00000198330 TRGV7 ENSMUST00000103553

```


For two genes that are identical except for extra bases on the 3' end, only the longer version was retained. List of affected genes:

```
IGHD2-5 ENSMUST00000178549 IGHD5-2 ENSMUST00000179166 TRAV11D ENSMUST00000103648 TRAV12D-1 ENSMUST00000181360 TRAV12D-2 ENSMUST00000197007 TRAV13D-2 ENSMUST00000197954 TRAV14D-1 ENSMUST00000181038 TRAV14D-2 ENSMUST00000196802 TRAV15D-2-DV6D-2 ENSMUST00000199800 TRAV3D-3 ENSMUST00000196023 TRAV4D-3 ENSMUST00000103592 TRAV4D-4 ENSMUST00000103600 TRAV5D-4 ENSMUST00000179701 TRAV6-6 ENSMUST00000103584 TRAV7-2 ENSMUST00000103636 TRAV7D-5 
```

<LinkableSection id={"cr5-0"} nested={true} title={"CR 5.0"}></LinkableSection>

The recommended V(D)J reference packages for human and mouse have been updated from v4.0-5.0. The changes to the V(D)J reference sequences are listed below:

HUMAN:

```
Replace IGKV2D-40, whose leader sequence appears to be truncated.
Delete IGKV2-18, which is probably a pseudogene.
Delete IGLV5-48, which is truncated on the right.
Delete TRBV21-1, which has multiple frameshifts.
Add IGHV4-30-4, which was missing.
Add IGKV1-NL1, which was missing.
Add IGHV4-38-2, which was missing.
```

MOUSE:


```
Delete TRAV23, which is frame-shifted.
Delete the first base of the constant region gene IGHG2B.
Make a six-base insertion in IGKV12-89, based on empirical data.
Correct IGHV8-9, whose amino acid sequence showed the canonical C at the end of FWR3 as S. This is consistent with 10x data.
Add an allele of IGKV2-109, which was missing.
Add IGKV4-56, which was missing.
Add IGHV1-2, which was missing.
```


<LinkableSection id={"cr4-0"} nested={true} title={"CR 4.0"}></LinkableSection>

Recommended V(D)J reference packages for human and mouse have been updated from version 3.1.0 to 4.0.0. The changes to the V(D)J reference sequences are listed below:

* Remove the first base of the C region in certain cases. In these cases we observe that in most transcripts, the J region and C region overlap by exactly one base.
* Add an allele of the gene IGHJ6 to the human V(D)J reference.


<LinkableSection id={"cr3-0"} nested={true} title={"CR 3.0"}></LinkableSection>

Updates to prebuilt reference: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/3.1/advanced/built-in-refs

Transcriptome reference v1.2.0 to v2024-A and V(D)J reference v3.0 to v7.1

Reference Release Notes

Release Notes for Cell Ranger

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

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

Fixed RNA Profiling

What is Cell Ranger?

<Text as={'p'} size={'small'} weight={'medium'}>Cell Ranger v8.0 introduces support for the analysis of GEM-X libraries. 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.