Question: Can I analyze only the Gene Expression data from my single cell multiome experiment?
Answer: Yes, it is possible to analyze just the individual GEX libraries from a multiome assay using cellranger count. It requires v4 or newer of Cell Ranger to be installed on your system.
In addition, the following flags need to be specified for the software to correctly recognize and process the GEX data.
1. The --include-introns flag is necessary for Cell Ranger versions before 7.0 (--include-introns mode is on by default after Cell Ranger v7.0), since input type is nuclei for the multiome assay. It is enabled by default in the multiome pipeline (Cell Ranger ARC) but needs to be specified when running the single library analysis using just Cell Ranger for gene expression.
2. The type of assay chemistry needs to be specified to distinguish between a GEX library of a multiome assay vs standalone single assay GEX library. The specification of assay chemistry type using the --chemistry flag differs depending on the version of Cell Ranger and it is as follows:
Cell Ranger v4:--chemistry=JAG-v1
Cell Ranger v5+:--chemistry=ARC-v1
Starting Cell Ranger 7.1+, we displayed --chemistry=ARC-v1 in the count and multi help text and support site. You will also see an alert in the web summary to remind you. If you are using Cloud Analysis, this article has detailed instructions: How can I analyze only my Multiome Gene Expression library with Cell Ranger on 10x Genomics Cloud Analysis?
Alternatively, if you have already run cellranger-arc count to analyze your multiome experiment, and find the ATAC library to be low quality, you can look at an GEX-only web summary. The standalone GEX web summary can be found in the intermediate folder at SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/files/web_summary.html
Related article: Can I analyze only the ATAC data from my single cell multiome experiment?
Note: This type of analysis is not officially supported. We do not recommend or advise the analysis of single modalities from the multiome assay. The main benefits of the multiome assay i.e. joint cell-calling and feature linkages will not be available when analysis is carried out in this way.