Question: Can I analyze only the Gene Expression data from my single cell multiome experiment?
In addition, the following flags need to be specified for the software to correctly recognize and process the GEX data.
--include-introns flag is necessary 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:
Cell Ranger v5+:
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.