Question: Is it possible to combine or compare fixed RNA profiling data (FRP) with 3’ (or 5’) single cell gene expression (GEX) data? Can I use Cell Ranger aggr to do so?
It is possible to integrate FRP and 3’ (or 5’) GEX data. However, because the chemistries are fundamentally different (probe-based v.s. reverse transcription-based), significant batch effects are expected when combining the two types of data. Therefore, correction of the batch effects is needed if you want to analyze the two types of data together.
Internally, we have used a third-party tool, Harmony, for batch effect correction when combining FRP with 3’ GEX data, and it worked well for the samples we analyzed. Users may also choose to explore other batch correction tools developed by the community. We have an analysis guide article (Batch effect correction) that may provide some pointers on this topic. Note that the support we can provide on third-party software tools is very limited, so if you encounter issues with these tools, please contact the developers directly.
Using Cell Ranger aggr for combining FRP and 3’ (or 5’) GEX is not officially supported but possible. Please see the table on this page for supported and unsupported data combinations for Cell Ranger aggr. Note that the chemistry batch correction algorithm in Cell Ranger aggr was specifically intended to correct for systematic variability in gene expression profiles caused by different versions of the same Single Cell Gene Expression chemistry. Therefore, it is likely not going to work well for correcting batch effects between FRP and 3’ (or 5’) GEX data.