Frequently Asked Questions

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10x Genomics Cloud CLI
Project transfers and collaboration
Analyses and supported products
Data management
Citations
Browser Support
Operating Systems

10x Genomics Cloud CLI

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

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

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 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.


Analysis and supported products

What products and analysis pipelines are supported?
Currently, we support analyzing Single Cell Gene Expression (3' and 5') and Single Cell V(D)J libraries, including Feature Barcode Technology, using the Cell Ranger count, vdj, aggr, and reanalyze pipelines. We also support analysis of Single Cell Multiome datasets using Cell Ranger ARC count, aggr, and reanalyze. For more information on analysis pipelines available on Cloud Analysis, visit the Supported Products page.

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

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

For Cell Ranger ARC analysis, Cloud Analysis provides:

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

Can I use a custom reference?
Yes, custom references are supported in Cloud Analysis. Currently, you must build a reference locally using the Cell Ranger mkref 3.1 or later, Cell Ranger mkvdjref 3.1 or later, or Cell Ranger ARC mkref pipelines and then upload the output directory to Cloud Analysis. In the future, we plan to expand our features and offer additional methods of adding custom references to your account.

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 Cell Ranger, 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.


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 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, 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:


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:

For example:

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


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:

Supported tablet browsers:


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:

Learn more about uploading files using the 10x Genomics Cloud CLI here .