cellranger aggr is unable to combine cellranger multi output
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Hi,
I am currently using cellranger to process some 10x datasets which were sequenced with Total-seq A. Unfortunately, the antibody to sample assignment was inconsistent with some even having different antibody combinations. I realized that for the cellranger multi runs the cmo reference is also added to the feature reference in the molecule_info.h5 which causes aggr to raise an error and abort. I for now resorted to concatenating the data manually using AnnData with the sample_feature_bc.h5 file but I keep getting very weird results when using scanpy's umap. I am yet to investigate why this is and I also do not completely understand how aggr works but I wonder if there is any magic happening when using aggr as compared to plain conatenation of the adatas.
In any case, I guess this might help future users who are in the same situation as me ;)
Nevermind, I had a bug in my config file generator which caused the same sample being analysed multiple times resulting in weird umap artifacts. Anyway I guess knowing that you also should use the same CMO reference might help someone (I hope)