If I wanted to follow the integrated analysis of two datasets (control vs stimulated) tutorial, should I follow QC/clustering tutorials for each dataset separately first? Or does the integrated analysis already include all of those? Thanks in advance.
It may be better to merge the datasets upstream of Seurat: in the past, I think I've tried merging of 2 unfiltered tables at a time, but I think I ran into memory problems with that strategy.
One option would be to use cellranger aggr, but please note that you'll need to use the --normalize=none parameter to get the same quantifications as you would for the samples individually.
In the past, I could use cellrangerRkit with the load_cellranger_matrix() and load_cellranger_analysis_results() functions. However, I see a note that indicates this functionality may not be supported for newer protocols. So, I'm not sure what is the best advice, if using a newer protocol (and a newer version of Seurat).
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