I have some question about TCR sequencing data.
For the result that I got from cellranger processed following tutorial here: https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-vdj, there is one file called clonotypes.csv.
This file contains summary information of TCR clonotypes for one sample and is from filtered_contig_annotations.csv directly.
And in order to know how this clonotypes.csv result made, I summarized it from filtered_contig_annotations.csv in R and got almost the same result.
In clonotypes.csv, each clonotype only shows its cdr3s_aa and cdr3s_nt.
Actually, every clonotype contains a-chain (TRA) and/or b-chain (TRB), cdr3s_aa, cdr3s_nt and TRA/TRB'S V(D)J genes.
So, for my opinion, each clonotype should be defined by at least six parts.
But I don't know why it only contains two parts: cdr3s_aa and cdr3s_nt.
If we can use this two information to represent one clonotype, there will be many duplicates among these all colontypes.
If not, clonotypes.csv, is indeed produced from cellranger.
So my question is, how to define one clonotype and to do next step analysis, for example, find public clonotype, overlapping between different antigen specificities.
Thanks a lot.
