Question: My samples are analyzed with Cell Ranger v7.2. Should I upgrade to using the latest Cell Ranger v8.0?
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 note pages. If you already have data analyzed with Cell Ranger v7.2, you might wonder if it is necessary to update to Cell Ranger v8.0. Here is some general guidance regarding each library type:
Single Cell Gene Expression:
It is not required to rerun analysis with Cell Ranger v8.0 for Gene Expression dataset. There are minor changes in cell calling (link) which will result in slight delta in the cell calls. However this should only impact samples with high UMI count cells. Unless otherwise specified, we do not anticipate significant change in results. We analyzed our 10k PBMC dataset using Cell Ranger v7.2.0 and v8.0.0, and the table below summarizes some of the key metrics and they are consistent:
Metrics |
Cell Ranger v7.2.0 (multi) |
Cell Ranger v8.0.0 (multi) |
estimated number of cells | 11,999 | 11,999 |
mean reads per cell in library | 41,369 | 41,369 |
median reads per cell in sample | 33,876 | n.a |
mean reads per cell in sample | n.a | 39,033 |
median UMI counts per cell | 10,178 | 10,178 |
median genes per cell | 3,266 | 3,266 |
However if you are using GEM-X data, please upgrade to Cell Ranger v8.0. Analysis of GEM-X data is only supported in this version.
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). Also if you would like to take advantage of the new improvements described here, you may consider trying Cell Ranger v8.0.
Feature Barcoding (3' Cell Multiplexing, Antibody Capture and CRISPR):
For all CRISPR libraries, it is encouraged to upgrade to Cell Ranger v8.0 due to the substantial runtime improvements. For rest of the feature barcode libraries, it is not required to rerun analysis with Cell Ranger v8.0 because there are no significant changes in the algorithm and do not expect any change in results.
V(D)J:
Rerunning analysis using v8.0 should not be required, unless you are encountering any critical failure modes within the VDJ pipeline.
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 v7.1. Should I re-run analysis using the latest Cell Ranger v7.2 ?
Products: Single Cell Gene Expression, 3' Cell Multiplexing, Single Cell Gene Expression Flex, Single Cell Immune Profiling
Last Updated: Mar 2024