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 with only one chain?

Answer: The Cell Ranger pipeline does not filter out contigs with only one productive chain, as seen in our example datasets.

There are many reasons why you may see only one chain in a cell that should contain two chains:

1. mRNA transcript could not be detected by the assay: The mRNA transcripts for the missing chain may have been present in the cell, but not picked up by the assay. This is especially true of transcripts that have low expression.
2. No contig assembly: Some transcripts picked up by the assay may fail to get assembled into contigs.
3. Not marked as productive: Some assembled contigs may fail to be marked as productive. Only productive chains are displayed in the filtered results. Look in the all_contig_annotations.csv file to find contigs that are not marked as productive.
4. In rare cases, cells may only express one chain.

If a majority of your clonotypes consist of only one chain, there may be an issue with your sample.