Release Notes for Cell Ranger

Release Notes for Cell Ranger v1-v3.1 (Archived)

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" labelWeight="medium" size={{height: "40px", 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: "36px", width: "150px"}} labelWeight="medium" 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" labelWeight="medium" size={{height: "36px", 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" labelWeight="medium" size={{height: "36px", 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>

These references were created from V(D)J genes in Ensembl build 94, using both gtf and gff3 files, which provide slightly different information. The process is mechanical, and supplemented by manual edits, which we describe in detail here. There are two cases where we created unofficial gene names, and these should ultimately be replaced by official names.

One consequence of these changes is that all V gene sequences now begin with a start codon ATG. (This lies in the leader sequence coding for a signal peptide that is cleaved off).

For the prebuilt references, pseudogenes are excluded, except where we think the pseudogene labeling is incorrect, for specific instances described below.

Human V(D)J gene edits:

- Deleted TRBV6-3 because it is not in the Ensembl GTF and is nearly identical to to TRBV6-2.
- Deleted TRGV11 and IGHV1/OR15-9 because they are labeled non-functional by NCBI.
- Allowed TRAJ8, TRAV35 and TRBV21-1 even though they are labeled pseudogenes, because they are observed in productive pairs.
- Added TRAJ15, TRBD2, TRBV11-2 and TRGV11 because they are observed in productive pairs.
- Added IGHV1-8, IGKV2-18 and IGLV6-57 because they are observed in productive pairs.
- Added 1 base to the right of TRAJ36 because otherwise annotations fail the in-frame requirement for productive contig, which all other observed human and mouse J genes satisfy.
- Trimmed 3 bases from the right of TRAJ37 because otherwise one finds a three-base indel when one annotates the J/C junction (in observed data).
- Trimmed 89 bases from the left of IGLJ1, because these bases are not part of the actual J segment.
- Trimmed 104 bases from the left of IGLJ2, because these bases are not part of the actual J segment.
- Trimmed 113 bases from the left of IGLJ3, because these bases are not part of the actual J segment.
- Trimmed 57 bases from the left of TRBV20/OR9-2, because these bases are not part of the actual V segment.
- Added an alternate form of TRBV20-1, differing from the reference by a 3-base insertion, because we observe this form (here and below, we use the same name for the alternate inserted form).
- Added an alternate form of TRBV7-7, differing from the reference by a 15-base insertion, because we observe this form.

Mouse V(D)J gene edits:

- Deleted IGHV1-67, because it is labeled a pseudogene by NCBI.
- Added IGHV12-1, because we observe this gene in data.
- Added a V gene observed in two BALB/c datasets, aligning to an unplaced sequence in the BALB/c whole genome assembly, and we unofficially named this gene IGHV1-unknown1.
- Added a form of TRAV4-4-DV10 seen in BALB/c.
- Added a form of TRAV13-1 or TRAV13D-1 seen in BALB/c, and arbitrarily labeled TRAV13-1.
- Added a very common alternate splicing between the first exon of TRBV12-2 and the second exon of TRBV13-2, which we unofficially named TRBV12-2+TRBV13-2.
- Added an alternate form of TRAV16N, differing from the reference form by having a 3-base insertion, because we observe this in data.
- Added an alternate form of TRAV6N-5, differing from the reference by a 3-base insertion, because we observe this in data.
- Added an alternate form of TRAV13N-4, differing from the reference by a 15-base insertion, because we observe this in data.
- Added an alternate form of TRBV13-2, differing from the reference by a 21-base insertion, because we observe this in data.

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

Reference Release Notes

Updates to new versions of Cell Ranger are documented separately. 
<CTAButton href="/support/software/cell-ranger/latest/release-notes/cr-release-notes" label="Release Notes" size={{height: "40px", width: "250px"}} labelWeight="medium" icon="external-link" target="\_blank" mode="light" /> 

<LinkableSection id={"human"} title={"Human Models"}>
<LinkableSection id={"human-v1"} nested={true} title={"human_pca_v1_beta (September 24, 2024)"}>
Go to the [Cell Annotations Algorithm](/support/software/cell-ranger/latest/algorithms-overview/cr-cell-annotation-algorithm#human-models) page for a description of the `human_pca_v1_beta` model.
</LinkableSection>
</LinkableSection>
<LinkableSection id={"mouse"} title={"Mouse Models"}>
<LinkableSection id={"mouse-v1"} nested={true} title={"mouse_pca_v1_beta (December 4, 2024)"}>
Go to the [Cell Annotations Algorithm](/support/software/cell-ranger/latest/algorithms-overview/cr-cell-annotation-algorithm#mouse-models) page for a description of the `mouse_pca_v1_beta` model.
</LinkableSection>
</LinkableSection>

Release notes for Cell Ranger's automated cell type annotation models

Automated Cell Type Annotation Models Release Notes

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

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Cell Ranger

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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

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

Characterize tumor cells

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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

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multi (3'/5'/Flex)

count (GEX + Antibody/CRISPR)

vdj (VDJ-T/B only)

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Learn more about the output files generated by Cell Ranger

Outputs

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Gene Expression

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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={{
 flexDirection: 'column',
 gap: '0.5rem'
}}><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>

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