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• Plotting Clonotype ID frequency, as seen below, for the gene expression node (Cell counts as the top bar chart) and VDJ node (VDJ counts as the bottom bar chart), highlights the difference between the two nodes (where 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 as a cell and this can affect these 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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Tips for Figure Making

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