Could anyone inform me about the best approach for merging 2 technical replicates from the same 10x cDNA library, but run on different sequencers? Since the same cell barcodes are detected across both runs for many reads, I would like to merge them together while still accounting for batch effects.
Current approaches with Seurat, etc. assign new names to duplicated cell barcodes while merging counts or normalized data, treating the sample as though it was derived from two distinct cDNA libraries. This seems less accurate and reduces the actual read depth per cell for experiment. If the samples were run on the same instrument, I would otherwise just merge the two matrices and sum counts from identical barcodes (assuming that the technical variation was minimal).
Thanks for the help!