Question: Is there an obvious way of telling which barcodes contain multiple cells (multiplets) for V(D)J libraries?
Answer: At this time there is no good way to identify GEMs with multiple cells in the V(D)J library. We estimate the multiplet rate for V(D)J libraries to be the same as gene expression libraries.
Each cell-associated barcode should contain one productive TRA and one productive TRB contig. Barcodes with multiple alpha/beta chains (in the case of TCR) may indicate multiplets. However, the probability of multiple GEMs containing identical multiple chains is very low. Therefore, if multiple cells with the same clonotype have more than one alpha/beta chain, they are unlikely to be multiplets.
In general, the rate of true biological double-TRB or double-TRA cells is low. If only one cell has multiple alpha or beta chains, it could be a multiplet, a barcode collision event, a PCR chimera, or a true biological phenomenon. There is no way to be 100% certain.