Question: My samples are analyzed with Cell Ranger v8.0. Should I upgrade to the latest Cell Ranger v9.0?
Answer: In general, we recommend using the latest Cell Ranger release from our downloads page, due to added features, general improvements, and bug fixes. For every new release, we have a high level overview of changes in our release notes pages. If you already have data analyzed with Cell Ranger v8.0, you might wonder if it is necessary to update to Cell Ranger v9.0. Here is some general guidance regarding each library type:
Single Cell Gene Expression: It is not required to rerun analysis for Gene Expression datasets with Cell Ranger v9.0. There are minor changes in cell calling (link) which will result in slight change in the recovered cells. However, we do not anticipate significant change in results. We analyzed our 10k PBMC dataset using Cell Ranger v8.0.1 and v9.0, and the table below summarizes some of the key metrics and the delta is minimal. The slight decrease in the number of recovered cells in Cell Ranger 9.0, is due to a change in the empty drops false discovery rate threshold (lowered to 0.001). This update improves the sensitivity as reflected in the median UMI counts and median genes per cells metrics.
| Metrics |
Cell Ranger v8.0.1 (multi) |
Cell Ranger v9.0.0 (multi) |
| estimated number of cells | 11,994 | 11,979 |
| mean reads per cell in library | 41,386 | 41,438 |
| median UMI counts per cell | 10,278 | 10,290 |
| median genes per cell | 3,314 | 3,315 |
Note: If you are working with On-Chip Multiplexing (OCM) data, upgrading to Cell Ranger v9.0 is required regardless of the library type, as analysis of OCM data is supported starting with this version. Additionally, if you like to take advantage of the newly introduced annotate pipeline in Cell Ranger v9.0, we recommend upgrading.
Single Cell Gene Expression Flex: Similar to Gene Expression, rerunning data analysis is not necessary for the Singleplex Flex libraries (with or without Antibody Capture) and Multiplex Flex libraries (with or without Antibody Capture) unless you want to leverage the updates in the 2024A probe set reference files and other parameters (see release updates here). Additionally, if you would like to take advantage of the cell calling improvements for sub-pooling experiments you may consider upgrading to Cell Ranger v9.0.
Feature Barcoding (3' Cell Multiplexing, Antibody Capture, CRISPR): For feature barcode libraries, re-running analysis with Cell Ranger v9.0 is not required, as there are no significant changes in the algorithm affecting the performance and results, outside of hashing. However if you plan to run hashing analysis in Cell Ranger we recommend upgrading to Cell Ranger v9.0 to take advantage of the streamlined analysis workflows. Please see here for more guidance on running the pipeline.
Note that for an antibody-only analysis, a transcriptome reference is no longer needed. If this benefits your project, please consider upgrading to Cell Ranger v9.0 for optimized compatibility and improved workflows.
V(D)J: It is recommended to upgrade to Cell Ranger v9.0 due to the considerable VDJ algorithm changes implemented in Cell Ranger v9.0. Please see the list of VDJ algorithm updates here.
The guidance above is based on our internal testing results. If you have concerns regarding your specific sample, you might want to run some comparisons using your own data. Also, feel free to reach out to us at support@10xgenomics.com, if you have any questions.
Related article: My samples are analyzed with Cell Ranger v7.2. Should I upgrade to using the latest Cell Ranger v8.0?
Products: Single Cell Gene Expression, 3' Cell Multiplexing, Single Cell Gene Expression Flex, Single Cell Immune Profiling
Last Updated: Dec 2024