Cell Ranger version 7.0.0 is now available as the default Cell Ranger version in Cloud Analysis! Cell Ranger 7.0 includes support for Fixed RNA Profiling datasets. Learn more about the new Fixed RNA Profiling kit within the Cell Ranger Documentation for Fixed RNA Profiling and read about the changes in Cell Ranger 7.0.0 in the Cell Ranger Release Notes.

Additionally, you can now add custom library metadata to your aggr analyses in Cloud Analysis (e.g. lab or sample origin). These custom library annotations do not affect the analysis pipeline but can be visualized downstream in the Loupe Browser.

This update contains an exciting expansion: Cloud Analysis is now available in Canada!

We have also fixed a number of small bugs and added new functionality to the Web Uploader in this release.

A Web Uploader tool is now available on Cloud Analysis, enabling you to quickly upload FASTQ files using drag-and-drop functionality in your web browser, bypassing the command line interface (CLI) tool. The CLI option is still available, and may be preferable for large numbers of files.

Cell Ranger ARC 2.0.0 and 2.0.1 are now available on Cloud Analysis. This pipeline enables the analysis of 10x Genomics Single Cell Multiome datasets.

Analysis of Targeted Gene Expression data is now supported in Cloud Analysis! You are also able to aggregate datasets that were generated using our CellPlex Multiplexing Solution.

Finally, we added the ability to automatically generate commands to download output files using the 10x Genomics Cloud CLI.

Read more about the different download options available in Cloud Analysis on our file download documentation.

A new version of the 10x Genomics Cloud CLI is now available! This release (version 1.2.0) allows you to download your analysis output files directly through the command line. This download option contains benefits over the alternatives, such as the ability to resume failed or interrupted downloads.

Additionally, this version of the 10x Genomics Cloud CLI fixes a bug where FASTQ files that are larger than 50 GB would stall using the default command.

To download this update, visit the 10x Genomics Cloud CLI documentation.

You are now able to aggregate your Single Cell V(D)J libraries on Cloud Analysis! After your cellranger vdj analyses complete, select the 'Aggregate Multiple Analysis' button above the Analyses table to begin the setup process.

Cell Ranger version 6.1.2 is now available as the default version in Cloud Analysis, while older versions remain available. This Cell Ranger release contains a number of bug fixes. Read about the changes in Cell Ranger 6.1.2 in the Cell Ranger Release Notes.

We also made it easier to assign library and feature types to your FASTQ sets. Select any number of rows from the FASTQ table inside each project, then use the dropdown selector at the top of the table to assign values to multiple FASTQ sets at the same time!

We've updated Cloud Analysis to provide substantial speed and responsiveness improvements to projects with large numbers of FASTQ files.

The cellranger multi pipeline is now available on Cloud Analysis! Analyze your datasets that use cell multiplexing, or analyze datasets that include V(D)J repertoire, cell surface protein, antigen specificity and 5' gene expression data together in a single pipeline. Learn more about cellranger multi on the Cell Ranger Documentation for Single Cell Gene Expression and on the Cell Ranger Documentation for Single Cell Immune Profiling.

When you register your Chromium X/iX, you can now view useful summary statistics about your instrument usage on 10x Genomics Cloud!

Cell Ranger version 6.1.1 is now available as the default Cell Ranger version in Cloud Analysis. This release contains a bug fix for the cellranger vdj pipeline that would cause it to fail in certain circumstances.

You are now able to view and download detailed run log information for your Chromium X or Chromium iX if you choose to automatically upload logs from your device.

Cell Ranger version 6.1.0 with High Throughput Kit support is now available as the default Cell Ranger version in Cloud Analysis! Learn more about the new High Throughput Kit within the Cell Ranger Documentation for HT and read about the changes in Cell Ranger 6.1.0 in the Cell Ranger Release Notes.

We are excited to launch a newest service on the 10x Genomics Cloud: the 10x Genomics Cloud Instruments portal is available today at https://cloud.10xgenomics.com/instruments/. This platform is used to register your Chromium X, access the latest firmware and documentation, and soon you will be able to view and download your instrument's run logs if you choose to register your Chromium X/iX to your 10x Genomics Cloud account!

Cell Ranger version 6.0.2 is now available as the default Cell Ranger version in Cloud Analysis. Details about the changes in Cell Ranger 6.0.2 are available in the Cell Ranger Release Notes. Older Cell Ranger versions, including versions 6.0.1 and 6.0.0, are still available for use in Cloud Analysis.

We've added support for custom mouse panels with our Targeted Gene Expression product! Compatible with Single Cell Gene Expression and Immune Profiling assays, you can now design and order a fully custom mouse panel with our Custom Panel Designer!

Support for custom references is now available in Cloud Analysis! You can upload a custom reference transcriptome that you have created with either the cellranger mkref or cellranger mkvdjref pipelines and use this as a reference in your analyses. In the future, we will be expanding this feature and making it even easier for you to add non-human and non-mouse references to your 10x Genomics account for use in analyses.

To learn more about use of custom references in Cloud Analysis, please refer to our documentation.

This update includes the newest Cell Ranger release and support for additional pipelines and products.

• Cell Ranger version 6.0.1 is now available as the default Cell Ranger version in Cloud Analysis. This release includes a number of general improvements and bug fixes that are documented in the Cell Ranger 6.0 Release Notes. Older Cell Ranger versions are still available to use.
• Aggregation of analyses including Feature Barcode data is now supported in Cloud Analysis.
• Single Cell 3' Gene Expression LT (Low Throughput) datasets are now officially supported in Cloud Analysis.

You can now analyze your Feature Barcode data in Cloud Analysis!

• Upload your datasets that include Cell Surface Proteins, Antigen Specificity, or CRISPR Guide Capture, then setup and run count (Feature Barcode) in Cloud Analysis.
• Improved data management: delete FASTQ files, analyses, and whole projects from your account.
• We have added new output files with ongoing free storage and downloads. See the full list of files with free ongoing storage here.

Cell Ranger 6.0 is now available in Cloud Analysis! This is the new default Cell Ranger version for count, aggr, reanalyze, and vdj pipelines. You can still select older versions when setting up your analysis. For full details about supported pipelines and versions in Cloud Analysis, read more here. To learn more about what's new in Cell Ranger 6.0, please read the Cell Ranger 6.0 Release Notes.

We fixed an issue where the Cell Ranger version used to analyze data was the most recent version 5.0.1 but the user interface displayed version 5.0.0. We've also updated our Windows installation and usage instructions for the 10x Genomics Cloud CLI.

Cloud Analysis is now available to all users in the United States! This update contains a number of exciting new features including:

• A beta version of the 10x Genomics Cloud CLI for Windows is now available. You can download the Windows versions here.
• You are now able to download your FASTQ files. Select a row in the FASTQ table and click the download icon above to reveal curl and wget commands.

We've added support for the cellranger vdj pipeline, and now have support for Cell Ranger versions 5.0, 4.0, & 3.1 in Cloud Analysis.

• Single Cell V(D)J libraries can now be analyzed on Cloud Analysis using the Cell Ranger V(D)J pipeline.
• Cell Ranger version 5.0 is the new default version for the count, aggr, reanalyze, and vdj pipelines. When you configure the settings for an analysis, you can still select versions 4.0 or 3.1 if you would like to use an older version of Cell Ranger.
• Improvements to the process of aggregating multiple analyses. Now, you can only select analyses that are eligible for aggregation. We filter out reanalyze and aggr analyses, which are not valid inputs to Cell Ranger aggr.

We fixed a small issue in our design tool that resulted in some 121 nucleotide baits when designing for exogenous sequences, while the maximum length should be 120 nucleotides.

The issue should not have impacted any experimental results, but it could have impacted turnover time when ordering this panel through oligo providers such as IDT.

We've addressed a few small bugs that have been identified thanks to our Early Access users.

• Fixed a bug in the 10x Genomics Cloud CLI that prevented users from attempting to retry failed uploads.
• Fixed a bug where users may encounter a blank page after transferring a project to another user.

We just announced compatibility of Targeted Gene Expression products with Visium Spatial Gene Expression! To go along with this announcement, we have also added a new Human Neuroscience Panel. You can now add on to this panel in a custom design with additional genes and exogenous sequences of interest. Pease note that fully custom panels are not supported for targeted experiments with Visium Spatial Gene Expression.

Cloud Analysis is now available for Early Access users! Cloud Analysis will make it easier than ever to access and run 10x software, track and manage your experimental data and share that data with collaborators and researchers.