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. 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 Pipeline Runner service can be successfully reached.

Details are available on the 10x Genomics Cloud CLI page under "Authentication".

What collaboration features are available? Can I share my projects or data with collaborators?
Pipeline Runner 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 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 Pipeline Runner 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.

What products and analysis pipelines are supported?
For the latest information on supported products and analysis pipelines available on Pipeline Runner, visit the Supported Products page.

What references are available?
Currently, Pipeline Runner provides the following references compatible with Cell Ranger Single Cell Gene Expression analysis:

• Human (GRCh38) 2024-A
• Human (GRCh38) 2020-A
• Human (GRCh38) v3.0.0
• Human (hg19) v3.0.0
• Mouse (GRCm39) 2024-A
• Mouse (mm10) 2020-A
• Mouse (mm10) v3.0.0
• Human and mouse (GRCh38 and GRCm39) 2024-A
• 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
• Rat (mRatBN7.2) 2024-A

For Cell Ranger V(D)J analysis, Pipeline Runner 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, Pipeline Runner provides:

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

For Space Ranger analysis (Visium HD and HD 3'), Pipeline Runner provides:

• Human (GRCh38) 2024-A
• Human (GRCh38) 2020-A
• Mouse (GRCm39) 2024-A
• Mouse (mm10) 2020-A
• Human and mouse (GRCh38 and GRCm39) 2024-A
• Rat (mRatBN7.2) 2024-A

For more information on these references, including build steps, visit the Cell Ranger references for Single Cell Gene Expression and Single Cell Immune Profiling data, the Cell Ranger ARC references for Single Cell Multiome data, or the Space Ranger references for Visium HD.

Can I use a custom reference?
Yes, custom references are supported in Pipeline Runner, 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 Pipeline Runner 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 Pipeline Runner, 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.

The Cell Ranger support website describes Cell Ranger's automated cell type annotation pipeline. You can run the pipeline 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 for the list of impacted regions.

The Normalization and Batch Correction Pipeline page addresses frequently asked questions regarding data integration options available on Pipeline Runner.

What are the options for uploading data to 10x Genomics Pipeline Runner?
Currently we support two options for uploading your data. You can either use the Web Uploader to quickly drag and drop files in your browser, or the Cloud CLI 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.

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.

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

• 10x Genomics Software Name and Version x.y.z using 10x Genomics Pipeline Runner

For example:

• 10x Genomics Cell Ranger 5.0.1 using 10x Genomics Pipeline Runner
• 10x Genomics Cell Ranger 4.0.0 using 10x Genomics Pipeline Runner

For more information about citation of 10x Genomics Software and products, please visit our citations page .

Is Pipeline Runner available in my region?

• Pipeline Runner is available globally (except for excluded territories), subject to applicable trade control restrictions. You may inquire about access to Pipeline Runner in your region by reaching out to 10x Support. Use of Pipeline Runner is subject to the 10x Genomics Cloud Services Terms.
• Paid services beyond the free usage limits are available only in the United States and Canada. See Usage outside the U.S. and Canada on our Billing page for more information.

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

Supported desktop browsers:

• Chrome
• Firefox
• Edge
• Safari

Supported tablet browsers:

• Chrome
• Safari

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 .