Question: If my clonotype has multiple alpha and beta chains (e.g. 1 alpha chain and 2 beta chains), what do I do? Should I discard the clonotype? Or just pick one of the chains?
Answer: A small fraction of T cells are known to express 2 alpha + 1 beta or 1 alpha + 2 beta chains (Ref1, Ref2). Similarly, there is evidence that some B cells express more than 1 heavy or light chain (Ref3, Ref4).
Therefore, if you find a large clonotype that expresses two chains of the same type, it is likely to be biologically relevant, not a technical artifact (e.g. multiple, PCR chimeras). If you see a more complex mixture of chain types such as 4 or more productive contigs, it is biologically unlikely and may be attributed to technical artifacts.
In the outputs from older Cell Ranger versions (3.0-), these multi-chain clonotypes are available, and you may choose to ignore them for downstream processing. Cell Ranger version 3.1+ assigns low confidence to all contigs in cells that express more than 4 productive chains - they are not included in the output clonotypes.