I have a couple questions about the output of cellranger aggr. In particular, I want to know if it performs any sort of batch correction. As far as I can tell, it does not. Does this mean I can run batch correction algorithms on the output? My understanding is that aggr is basically a glorified sc.concat()… Is that right?
In my experiment, I have two time points(Day 3 and Day 7) with two conditions (Wildtype vs Gene KO) each, which comprise a developmental process from basal cells to terminally differentiated cells. Each Time Point/Condition was loaded into a seperate GEM well(4 wells). I have noticed that my early progenitor cell types from different conditions (WT or KO) are contained in different leiden clusters. My concern is whether or not this is real biology or a symptom of a batch effect. If cell ranger aggr doesn’t run batch effect correction, should I do so?
Another question: I noticed that aggr performs total read normalization, and so I have chosen to omit this step from the standard scanpy QC pipeline during subsequent analyses. Is this the correct way to go about it?