Why do some clonotypes only have one productive chain?

Question: Each cell should have one TRA and one TRB chain, or one heavy and one light chain. Why do I have some clonotypes containing only one chain?

Answer: Our pipeline does not filter out contigs with only one productive chain. Our example dataset also has some clonotypes with only one chain.

There are several possible reasons why you may only see one chain in a cell while you are sure that it has two chains in reality:

1. The mRNA transcripts for the missing chain may have been present in the cell, but not picked up by the assay, especially if it is expressed in low levels. In some rare cases cells may only express one chain.
2. If the transcript was picked up by the assay, it might not have been assembled into a contig.
3. If the missing chain was assembled into a contig, it might not have been marked productive. Only productive chains are displayed in the filtered results. You could check the all_contig_annotations.json file to see if there are extra contigs not marked productive.

However, if all or the majority of the clonotypes are only consist of one chain, you might need to check if there is any issue with the sample.