Cell Ranger2.0, printed on 11/05/2024
The most high-level file that describes the clonotype frequencies for a sample is clonotypes.csv. See Annotations for details on this file. In order to compare clonotype frequencies between samples, you can match clonotypes using the cdrs_nt column, which contains the paired CDR3 nucleotide sequences for each clonotype.
Clonotype consensus sequences can be obtained from the consensus.fastq file, which also contains per-base quality scores.