Question: Can I use aggr to combine CellPlexed and non-CellPlexed data? Will there be batch effects?
Answer: The cellranger aggr pipeline supports the aggregation of 3' CellPlex v3.1 data with non CellPlex Single Cell 3’ v3.1 data. The cellranger multi pipeline generates a per sample sample_molecule_info.h5 file which is equivalent to molecule_info.h5 file from a cellranger count run. These files can be used as input to cellranger aggr pipeline.
Further, CellPlex protocol has additional wash steps. These wash steps may lead to depletion of more ambient mRNA from a CellPlexed sample as compared to a non multiplexed sample. This may then introduce small batch effects between CellPlex and non CellPlexed data. However, in our observation from internal data, the batch effects are fairly small and batch effect correction is not needed in most cases. If the results for each sample reveal obvious differences between the CellPlex vs. non CellPlex data, you can try cellranger aggr with chemistry batch correction, which may improve the mixing of the batches in the t-SNE visualization and clustering results.
If you are aggregating 3' v3.1 CellPlex samples with other chemistries (3’v2, 5’v2, etc.), you can treat the data similar to 3'v3.1 chemistry. For example, we recommend using chemistry batch correction when aggregating 3’v3.1 with 3’v2 chemistry. More information can be found in this knowledge base article: Can I aggregate gene expression data from different chemistries?