Question: How does the
cellranger vdj annotation algorithm determines which alpha chain gets matched to which beta chain for a particular cell barcode (especially if you have multiple productive alpha/beta contigs)? Or does the software not care about which chains are matched with which chains?
Answer: Our 5' Immune Profiling Solution for V(D)J repertoire aims at determining the V(D)J transcripts expressed for T and B cells at a single cell level. For T cells, each cell-barcode typically contains one productive TRA and one productive TRB chain, and for B cells, one productive heavy and one productive light chain. However, some fraction of T or B cells are known to express more than 1 chains of a type (see here).
Extra productive contigs produced by the assembler are less likely to be legitimate. So for each chain type, additional productive contigs (beyond the first) may be assigned as low confidence. Please see here for criteria for assigning contig confidence.
Beyond determining which chains come from which cell, Cell Ranger does not do pairing of chains with a cell.