Question: Is it possible to aggregate if we obtain nuclei and cellular data from the same sample?
Answer: Yes, it is possible to run cellranger aggr on nuclei and cellular data for the same sample. If running cellranger count or multi with --include-introns and if using the same reference on both these data types, there are no potential batch effects. It is also the recommended method to run cellranger aggr. In a few edge cases, the results are dependent on the cell type and tissue complexity, and using third-party tools like Seurat may be considered as these tools simply merge the raw feature barcode matrices and normalizes them. Please note that it is not possible to aggregate cellular datasets run without intron-mode with nuclei datasets.
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Products: Single Cell Gene Expression