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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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How the clonotypes are defined by cellranger vdj? #51

Closed YiweiNiu closed 10 months ago

YiweiNiu commented 4 years ago

Hi,

I am using cellranger vdj to analyze the single cell vdj libraries.

But I am confused about the clonotype definition by the tool.

From the documentation, it says

Cell barcodes are grouped together into clonotypes if they share the same set of productive CDR3 nucleotide sequences by exact match.

Does cellranger require that the CDR3 sequence of all the chains of IG or TR (e.g. IGH/IGK/IGL, TRA/TRB, TRD/TRG) are the samme or any one of these chains? If only the CDR3 match is only required by one of these chains, one cell may be assigned to different clonotypes.

I am new to this. Sorry if the question is too simple.

Thank you for your time.

Bests, Yiwei

WellJoea commented 4 years ago

I have the same question, especially when use the results for other softwares, such as vdjtools, immunarch.

vadimnazarov commented 4 years ago

Hello everyone, author of immunarch here.

At the moment we group clonotypes by CDR3 nucleotide sequence+V gene+J gene+Chain. It means that sequences with same CDR3 nucleotide sequence+V gene+J gene in a same chain counted as a singular entity and their barcodes are merged together. I would love to hear more about it as this poses an important problem. Traditional RepSeq studies are heavily dependant on the definition of the clonotype due to diversity of statistics such as the number of public clonotypes, gene usage and others.