The new release of Cell Ranger offers new functionality and enhancements for analyzing Feature Barcoding, V(D)J, and Gene Expression data from the Chromium Single Cell Immune Profiling and Chromium Single Cell Gene Expression Solutions.

Explore what’s new in Cell Ranger 3.1

For multi-omics data analysis:

• Perform cell surface protein and antigenspecificity analysis individually or in combination with gene expression and V(D)J clonotypes from the same single cell. Upgrade to Loupe Cell Browser 3.1.1 for multi-omics data visualization.
• Cluster cells in your single cell gene expression and Feature Barcoding datasets using the newly added UMAP (Uniform Manifold Approximation and Projection) algorithm.

Release notes for Cell Ranger
Download Cell Ranger
Release notes for Loupe Cell Browser
Download Loupe Cell Browser

For immune profiling data analysis:

• Lower your sequencing burden with analysis support for 26 x 91 sequencing read configuration for V(D)J libraries.
• Take advantage of V(D)J assembler improvements, resulting in increased sensitivity and more productive V(D)J pairs or receptors

Release notes for Cell Ranger
Download Cell Ranger

You are receiving this email as you engaged with 10x Genomics’ products or software. Download this software release to access additional data analysis capabilities.

Release Notes for Cell Ranger 3.1: Gene Expression & Feature Barcoding

Major Changes

• Feature Barcoding Only Analysis - It is now possible to run cellranger count using only Antibody Capture libraries. Previously, Cell Ranger required at least one GEX (or VDJ) library to run, even if the customer only wants to sequence their Feature Barcoding libraries (to reduce sequencing and library preparation costs or for other reasons). In particular, cell calling now works with antibody counts only, and all secondary analyses (PCA, t-SNE, UMAP, clusterings) work with antibody-only count matrix as well. More details are available on the Feature Barcoding Only Analysis page.

• UMAP based lower dimensionality projections of datasets analyzed by cellranger count are now produced in addition to the previously produced t-SNE projections. The projections are made available both as CSV files and as data that can be directly viewed in Loupe Cell Browser. The parameters for the projection can also be modified and experimented with using cellranger reanalyze. This alternate visualization method has become increasingly popular for visualizing single cell data since the earliest report that used it. For more details, see the description in the algorithms overview section.

• New Web Summary Look - The Cell Ranger web_summary.html file has been updated to match the styles and formats of other 10x products. Compared to the old version users will notice new fonts and some aesthetic changes in the new version.

Minor Changes

• Bug Fix: If equal numbers of reads with given Barcode / UMI combination map to two genes, the assignment of the Barcode / UMI are now considered ambiguous and not reported in molecule_info.h5 or the count matrix. Previously they were reported twice, once for each gene.
• Other minor bug fixes