
<LinkableSection id={"10-x-genomics-cloud-cli-046e78"} title={"10x Genomics Cloud CLI"}>

**How to reset your access token?**\
To reset your access token, run the following commands in order:

- `txg auth reset`: to delete any previously saved authentication tokens.
- `txg auth setup`: to set up a new authentication token interactively. Find your access token on your [Account Security page](https://cloud.10xgenomics.com/account/security). Do not share this access token or use this on a public computer.
- `txg auth verify`: to verify that the stored access token is valid and that the 10x Genomics Cloud Analysis service can be successfully reached.

Details are available on the [10x Genomics Cloud CLI page](/support/software/cloud-analysis/latest/tutorials/CA-cloud-cli-documentation-for-linux#authentication-ef1ec9) under "Authentication".

</LinkableSection>

<LinkableSection id={"project-transfers-and-collaboration-b7df54"} title={"Project transfers and collaboration"}>

**What collaboration features are available? Can I share my projects or data with collaborators?**\
Cloud Analysis allows you to transfer projects from one user account to another user account. In the Project Settings page of each project, you will find a place to enter the email address of the person you'd like to transfer the project to.

We expect to add more collaboration features over time, including the ability to invite multiple users to the same project.

Have ideas about collaboration features that you'd like to see? [Give feedback](https://10xgenomics.co1.qualtrics.com/jfe/form/SV_3L604WOrnTYI9W5?feature=collaboration%20tools&app=10x%20Genomics%20Cloud%20Analysis) to the team.

**Is there a limit on how many project transfers can be done?**\
Yes, each project can be transferred a maximum of three times. After three successful transfers, the project transfer functionality will be disabled for the selected project. Multiple transfers between two users will count as individual events.

**How does project transfer impact free usage limits?**\
Each time a project is successfully transferred to another Cloud Analysis user, the free usage limits are reset. The recipient of the project will receive 90 days of free storage for each file within the project starting from the date that the transfer completed. The recipient will also have the ability to run new analysis pipelines and download files as though this is a new project.

</LinkableSection>

<LinkableSection id={"analysis-and-supported-products-2f80de"} title={"Analysis and supported products"}>

**What products and analysis pipelines are supported?**\
For the latest information on supported products and analysis pipelines available on Cloud Analysis, visit the [Supported Products page](/support/software/cloud-analysis/latest/miscellaneous/CA-supported-products).


**What references are available?**\
Currently, Cloud Analysis provides the following references compatible with Cell Ranger Single Cell Gene Expression analysis:

- Human (GRCh38) 2020-A
- Human (GRCh38) v3.0.0
- Human (hg19) v3.0.0
- Mouse (mm10) 2020-A
- Mouse (mm10) v3.0.0
- Human and mouse (GRCh38 and mm10) 2020-A
- Human and mouse (GRCh38 and mm10) v3.1.0
- Human and mouse (hg19 & mm10) v3.0.0

For Cell Ranger V(D)J analysis, Cloud Analysis provides:

- Human (GRCh38) - v5.0.0
- Human (GRCh38) - v4.0.0
- Human (GRCh38) - v3.1.0
- Mouse (GRCm38) - v5.0.0
- Mouse (GRCm38) - v4.0.0
- Mouse (GRCm38) - v3.1.0

For Cell Ranger ARC analysis, Cloud Analysis provides:

- Human (GRCh38) - v2.0.0
- Mouse (mm10) - v2.0.0

For Space Ranger analysis (Visium HD), Cloud Analysis provides:

- Human (GRCh38) 2020-A
- Mouse (mm10) 2020-A

For more information on these references, including build steps, visit the [Cell Ranger references](/support/software/cell-ranger/downloads#reference-downloads) for Single Cell Gene Expression and Single Cell Immune Profiling data, the [Cell Ranger ARC references](/support/software/cell-ranger-arc/downloads#reference-downloads) for Single Cell Multiome data, or the [Space Ranger references](/support/software/space-ranger/downloads#reference-downloads) for Visium HD.

**Can I use a custom reference?**\
Yes, custom references are supported in Cloud Analysis, with the following caveats.

For Cell Ranger:

- Custom references must be generated with `cellranger mkref` v3.1.0 or higher. The `spaceranger mkref` references cannot be used in `cellranger count` or `cellranger multi`
- The pipeline version that is run in Cloud Analysis must be the same or more recent than the version of `mkref` used to generate the reference

For Cell Ranger ARC:

- Custom references must be generated with `cellranger-arc mkref` v2.0.0 or higher
- Only references generated with `cellranger-arc mkref` can be used

For Space Ranger:

- Custom references must be generated with `spaceranger mkref` v3.0.1 or later

**Can I upload a public 10x Genomics dataset from the Sequence Read Archive (SRA)?**\
In many cases, 10x Genomics datasets that are available at the Sequence Read Archive are compatible with Cloud Analysis, but you must first pre-process the files. For details on the types of datasets that are available and how to prepare your data, please view our [Knowledge Base guide](https://kb.10xgenomics.com/hc/en-us/articles/115003802691-How-do-I-prepare-Sequence-Read-Archive-SRA-data-from-NCBI-for-Cell-Ranger-).

</LinkableSection>

<LinkableSection id={"cell-annotations"} title={"Cell annotation pipeline (beta)"}>

The Cell Ranger support website describes [Cell Ranger's automated cell type annotation](/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-annotation) pipeline. You can [run the pipeline](/support/software/cloud-analysis/latest/tutorials/CA-creating-analyses#annotations) on the Cloud. 


The availability of automated cell annotation is subject to restrictions based on U.S. or local laws and regulations. See [regional restrictions](/support/software/cloud-analysis/latest/faqs/CA-frequently-asked-questions#regional-availability) for the list of impacted regions.

</LinkableSection>


<LinkableSection id={"data-management-25ffb1"} title={"Data management"}>

**What are the options for uploading data to 10x Genomics Cloud Analysis?**\
Currently we support two options for uploading your data. You can either use the [Web Uploader](/support/software/cloud-analysis/latest/tutorials/CA-web-uploader) to quickly drag and drop files in your browser, or the [Cloud CLI](/support/software/cloud-analysis/latest/tutorials/CA-upload-via-cli-for-linux) to upload files from the command line (which may be preferable for large numbers of files).

**Can I download my data?**\
Yes, you can download your custom references, images, FASTQ files, and analysis output files via `curl` and `wget` commands. Additionally, you may choose to download analysis output files through the browser. We recommend downloading all large files via `curl` or `wget`.

**What is 10x Genomics doing to secure my data?**\
We care about securing your data and protecting your user account. Here are some of the protocols and practices we have in place:

- Data is encrypted in transit and at rest using industry-standard protocols and ciphers.
- Multi-factor authentication is available to all of our users, and can be set up in the Account Settings page.
- Our platform undergoes routine independent assessments and penetration tests, covering functionality, business logic, common vulnerabilities, and reviews of security controls and requirements, including the OWASP Top 10 and ASVS.
- We utilize automated static and dynamic analysis tools to scan for vulnerabilities and potential security issues.
- Access to the platform and infrastructure is internally restricted and follows the principle of least privilege.
- A Security Operations Center team provides dedicated 24/7 monitoring of security-related events.

Learn more about how [10x Genomics secures customer data and user accounts on the cloud](/library/573c2b).

**Where are the 10x Genomics Cloud servers located?**\
Servers and data storage buckets are hosted by Amazon Web Services and are located in the United States.

</LinkableSection>

<LinkableSection id={"citations-a0dd5a"} title={"Citations"}>

**Do you have any guidance on how to cite datasets that were generated in Cloud Analysis?**\
To cite datasets that were generated in 10x Genomics Cloud Analysis, we recommend that you use the following format:

- 10x Genomics Software Name and Version x.y.z using 10x Genomics Cloud Analysis

For example:

- 10x Genomics Cell Ranger 5.0.1 using 10x Genomics Cloud Analysis
- 10x Genomics Cell Ranger 4.0.0 using 10x Genomics Cloud Analysis

For more information about citation of 10x Genomics Software and products, please visit our [citations page](https://support.10xgenomics.com/docs/citations) .

</LinkableSection>

<LinkableSection id={"regional-availability"} title={"Regional availability"}>

**Is Cloud Analysis available in my region?**

- Cloud Analysis is available globally except for Cuba, Iran, North Korea, Syria, Russia, Belarus, China, Hong Kong, Venezuela, and Ukraine. Using the Cloud Analysis services in excluded territories, or by persons that are subject to debarment or any list-based designations under U.S. or other applicable export controls laws and regulations, is a violation of the Cloud Analysis Service Terms and the applicable account will be terminated.
- While Cloud Analysis is currently unavailable in Ukraine, we expect that the services will be enabled in the future, with the exclusion of the regions of Crimea, Donetsk Regions of Crimea, and the city of Luhansk. You may inquire about access to Cloud Analysis in your region by reaching out to support@10xgenomics.com.
- Paid services beyond the free usage limits are available only in the United States and Canada. See [Usage outside the U.S. and Canada](/support/software/cloud-analysis/latest/miscellaneous/CA-billing#usage-outside-us-canada) on our Billing page for more information.

</LinkableSection>

<LinkableSection id={"browser-support-388a3e"} title={"Browser support"}>

**Which web browsers can I use to access 10x Genomics Cloud Analysis?**\
We recommend that you access Cloud Analysis through a recent version of a browser from our supported list, seen below.

Supported desktop browsers:

- [Chrome](https://www.google.com/chrome)
- [Firefox](https://www.mozilla.org/firefox)
- [Edge](https://www.microsoft.com/edge)
- [Safari](https://www.apple.com/safari)

Supported tablet browsers:

- [Chrome](https://www.google.com/chrome)
- [Safari](https://www.apple.com/safari)

</LinkableSection>

<LinkableSection id={"operating-systems-28e3c8"} title={"Operating systems"}>

**What systems can I upload custom reference and FASTQ files from?**\
Currently, we support uploading custom references and FASTQ files from Linux, macOS, and Windows 10.

Recommended Operating Systems:

- Ubuntu Linux 20.04
- macOS 10.15 and above
- Windows 10 build 17063 and above

Learn more about uploading files using the 10x Genomics Cloud CLI [here](/support/software/cloud-analysis/latest/tutorials/CA-cloud-cli-documentation-for-linux) .

</LinkableSection>


FAQs

Frequently Asked Questions

10x Genomics Cloud Analysis is a platform for data management, analysis, and collaboration to simplify and accelerate the interpretation of 10x Genomics datasets. Cloud Analysis makes it easier than ever to run 10x analysis pipelines and manage your experimental data.

Overview

Tutorials

Release Notes

Billing

Supported Products

Cloud Analysis

Learn how to create a free account using the two different log-in options.

Account creation

Upload input files into your projects using the Web Uploader.

Upload via Web Browser

Upload input files into your projects using the 10x Genomics Cloud CLI.

Upload via CLI

In addition to the pre-built human and mouse reference packages available in Cloud Analysis, you can upload and use your own custom references in your Cloud Analysis projects.

Upload a reference

After uploading input files into your project in Cloud Analysis, you are ready to analyze your data.

Create analyses

You are given four unique options for downloading your output files for each completed analysis. These options have certain benefits and limitations that make them appropriate for different circumstances.

Download output files

Cloud Analysis allows you to transfer projects from your user account to another user account.

Transfer projects

The 10x Genomics Cloud CLI is a command line interface (CLI) that allows you to upload input files to projects in your 10x Genomics account, create projects from the command line, and manage other tasks related to your 10x Genomics account.

CLI Documentation

10x Genomics Cloud Analysis is a platform for data management, analysis, and collaboration to simplify and accelerate the interpretation of supported 10x Genomics single cell and spatial datasets. Cloud Analysis makes it easier than ever to run 10x analysis pipelines and manage your experimental data.

What is Cloud Analysis?

<Text as={'p'} size={'small'} weight={'medium'}>If you are a member of a core lab or service provider, see <Anchor href={'/support/software/cloud-analysis/latest/getting-started/CA-guidance-for-cores'}>{'how Cloud Analysis can help improve your workflow.'}</Anchor><br/><br/>Explore our new <Anchor href={'/support/software/cloud-analysis/latest/tutorials/CA-cell-annotation-pipeline'}>{'beta pipeline for generating cell annotations'}</Anchor>, now available in Cloud Analysis! This feature will be fully integrated into the upcoming release of Cell Ranger.</Text>

Projects are where you upload data and run analysis pipelines. People typically create projects for each experiment. You can upload different samples to a single project.

Create Projects

Upload input files either directly from your web browser or via the 10x Genomics Cloud CLI.

Upload input files

After uploading, select the file sets that you want to work with. Then configure your pipeline settings and start the analysis.

Create Analyses

You can optionally receive an email when your analysis completes. When your results are ready, you can download the analysis outputs and explore your data using Loupe Browser or a variety of community-developed tools.

Download Results

10x Genomics pre-built human, mouse, and barnyard references are available. You may optionally upload your own custom references to use in the analyses on your account.

Optional workflow steps

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

Find answers to frequently asked questions, including information about browser and operating system support.

We regularly add new features to 10x Genomics Cloud. Find details about the updates and improvements on this page.

Find information about our free usage policies and optional paid services.