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UMI (Unique Molecular Identifier): random 10 bp nucleotide sequence that distinguishes which reads came from the same transcript.
Barcode: the unique identifier in each droplet which usually contains reads from a single cell.
Contig: assembled reads containing the same UMI and barcode that align to the same transcript sequence⁶.
Complementarity-Determining Region: CDR1, CDR2, and CDR3 are important in antigen binding of a T or B cell receptor.
CDR3 (Complementarity-Determining Region 3): CDR3 spans the V(D)J junction. There is one CDR3 nucleotide sequence for each V(D)J contig.
Clonotype: cells derived from a common ancestor during clonopoiesis which have a particular composition. The cells in a clonotype can have a different number of chains or different CDR3 regions but still be considered a single clone (CDR3 is a highly variable region used for binding; an example of different CDR3 regions would be from affinity maturation which can occur in memory B cells).

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Create a new project to upload your data. Ensure that you have transferred the filtered contig_annotations.csv file(s)² for each sample from either the cellranger vdj⁶ ⁷ or cellranger multi⁷⁸pipeline to the server, as well as the filtered feature barcode matrices in H5⁴ or MEX⁵ format from the cellranger multi pipeline for each sample if you have matching gene expression data.
Click Import, then select Import single cell V(D)J data

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Partek Flow Documentation