My samples are analyzed with Cell Ranger v7.0. Should I rerun analysis using the latest Cell Ranger v7.1?
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 v7.0, you might wonder if it is necessary to update to Cell Ranger v7.1. Here is some general guidance regarding each library type:
Single Cell Gene Expression:
In general, no need to rerun analysis with Cell Ranger v7.1 for Gene Expression dataset. We made some minor improvements in the cell calling, but in most cases, it only causes minimal (if any) changes in your results. Please see more details in this article.
Single Cell Gene Expression Flex:
Similar to Gene Expression, rerunning data analysis is not necessary. In most cases, the minor improvements in cell calling should only have minimal impact on the results. Please see more details in this article. We added the ability to estimate background signal level from genomic DNA, but this has no effect on the analysis results. Note that if you are analyzing single cell FFPE (scFFPE) data generated using the Flex kit, we recommend using Cell Ranger version v7.1.0 and later, as v7.1.0 has been validated and tested with scFFPE data analysis, while v7.0.1 and before have not.
Rerunning analysis should not be required, unless you noticed under-calling of B and T cell data (when analyzed together with GEX data), or odd clonotype grouping, such as a large clonotype with many chains. In Cell Ranger v7.1, the V(D)J algorithm implements better filter heuristics by leveraging Gene Expression data to retain more cells. These improvements may increase the number of cells called in VDJ data. Please see more detail in this article.
3’ Cell Multiplexing:
No need to rerun the analysis, unless your previous results have a large number of zero CMO UMI counts (shown as a tall ‘bar’ at 0 UMI for the CMO histogram). In Cell Ranger 7.1, we have improved tag assignment for samples with a large number of zero CMO UMI counts. Please see more details in this article.
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 firstname.lastname@example.org, if you have any questions.
Products: Single Cell Gene Expression, 3' Cell Multiplexing, Single Cell Gene Expression Flex, Single Cell Immune Profiling.