Question: What are the updates to cell multiplexing analysis in Cell Ranger v7.1? Do I need to upgrade the Cell Ranger version?
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 the release note pages.
If you already have CellPlex or general cell multiplexing data analyzed with Cell Ranger v7.0, rerunning analysis using Cell Ranger 7.1 is not necessary, unless you see a large number of cells with zero CMO UMI counts in your data.
The zero UMI counts can be observed using the plot titled “Histogram of CMO Count” in the web_summary.html. For example, in the plot below, we see a large number of cells with 0 UMI counts (indicated by the red arrow).
In Cell Ranger 7.1, we have updated the algorithm to filter these cells from the underlying model to improve overall tag assignment for the dataset.