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V(D)J recombination occurs in lymphocytes when T and B cells assemble variable (V), diversity (D), and joining (J) gene segments, contributing to the generation of receptors that recognize and respond to perturbations. V(D)J recombination produces clones of unique T cell receptor (TCR) chains or B cell receptor (BCR) chains giving rise to the diverse repertoire of T and B cell populations which are imperative to adaptive immune system function¹. The frequency of generated clones can be measured and explored, giving researchers a powerful view into variation, expansion, and diversity within the biological system. You can import filtered Contig Annotation CSV files² from the 10X 10x Genomics Cell Ranger V(D)J or multi pipeline³. If there is matching gene expression data, it can also be imported and analyzed within the same project. We recommend uploading the filtered feature barcode matrices as either the Hierarchical Data Format (H5 or HDF5)⁴ or Market Exchange Format (MEX)⁵. 

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• Plotting Clonotype ID frequency from the Cell counts and VDJ node counts nodes highlights the difference between the two nodes. In this example, the top plot is the number of cells per clonotype and the bottom plot is the number of V(D)J clonotypes present. Note that Cell Ranger does not always call the barcode a cell and this can affect frequencies when making comparisons between cell frequency per clonotype and barcode frequency per clonotype. An example of this would be clonotype1 when comparing the figure above and below. 

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