FAQ

Frequently Asked Questions

How are non-productive TCRs filtered?

It is possible that a minority of the TCR alignments result in non-productive TCRs. A TCR is considered non-productive if it has an out of frame junction sequence and/or an early stop codon and/or any defect described in the initiation codon, splicing sites and/or regulatory elements. By default, we do not perform any specific filtering for non-productive TCRs, considering that the minority of results of this kind can be neglected. In addition, we have found it is more common to see non-productive rearrangements in alpha chains, but we often observe that these are clonal, so they are likely the result of dual alpha-chain-expressing clonotypes rather than poor quality sequencing data. In any case, the results table at transcript level (sample_barcode_umi_results.csv) includes a column named productive (see output tables wiki), by which the user can filter out non-productive TCRs.

What happens when there are multiple TCR pairings in a cell?