Question: My samples are analyzed with Cell Ranger v7.1. Should I rerun analysis using the latest Cell Ranger v7.2?
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 v7.1, you might wonder if it is necessary to update to Cell Ranger v7.2. Here is some general guidance regarding each library type:
Single Cell Gene Expression: It is not required to rerun analysis with Cell Ranger v7.2 for Gene Expression dataset. There are no changes in cell calling and so we do not expect any change in results. We analyzed our 10k PBMC dataset using Cell Ranger v7.1.0 and v7.2.0, and the table below summarizes the main metrics:
| Metrics |
Cell Ranger v7.1.0 (multi) |
Cell Ranger v7.2.0 (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 | 33,876 |
| median UMI counts per cell | 10,178 | 10,178 |
| median genes per cell | 3,266 | 3,266 |
Following are some key parameters introduced in Cell Ranger v7.2:
- Ability to specify the output directory using
--output-dirparameter - Ability to subsample reads for chemistry detection using
detect_chemistry_sample_readsparameter in theparameters.tomlfile
If you would like to take advantage of the new parameters described here, you may consider trying Cell Ranger v7.2.
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 without Antibody Capture. However please note that Cell Ranger v7.2 is required for analysis of Flex data multiplexed with Gene Expression and Antibody Capture libraries.
3' Cell Multiplexing: It is not required to rerun analysis with Cell Ranger v7.2 for a 3' cell multiplexed dataset. There are no changes in tag calling and so we do not expect any change in results.
V(D)J: Rerunning analysis using v7.2 should not be required, unless you are working with BEAM (Antigen Capture) data and would like to combine antigen capture data between multiple samples.. Cell Ranger v7.2 supports the aggregation of BEAM libraries using cellranger aggr pipeline to combine and normalize the calculation of antigen specificity scores across multiple (or large samples) split across wells.
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: Oct 2023