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.
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Bios •
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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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