Question: How can I identify the different 10x libraries when analyzing a gene-barcode matrix from cellranger aggr?
Answer: In order to identify the 10X library source for the cells combined in cellranger aggr, leverage the concept of GEM groups. The GEM group is an integer that is appended to each barcode in the aggr gene-barcode matrix. For example, AGACCATTGAGACTTA-1 and AGACCATTGAGACTTA-2 are distinct cell barcodes from different libraries, despite having the same nucleotide sequence. The numbering of the GEM groups will reflect the order that the libraries were provided in the Aggregation CSV.