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Under Exploratory Analysis tasks is the Clonotype Frequency Plot task which will summarize the V(D)J node into plots of interest in the Data Viewer. Similar manual comparisons can be made in the Data Viewer. These may include determining the T cell receptor and B cell receptor chains that make up clonotypes in the samples, quantifying the clone diversity by frequency, comparing the immune repertoire between samples, and visualizing clones and gene expression data together on scatterplots like a UMAP. The example below shows the results from the Clonotype Frequency Plot task which is accessed by choosing to perform this task from the Single cell V(D)J node. In this case, the barcode frequency would be the frequency of clonotypes per cell, so there are 2 cells which have clonotype 5 (purple bar with information from hovering) and the clonotype 5 makeup contains two compositions (a heavy and light chain) which is seen in detail in the plot below

                                               Image Modified


References

  1. Tonegawa, S. Somatic generation of antibody diversity. Nature 302,575–581 (1983). https://doi.org/10.1038/302575a0
  2. https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/output/annotation#contig-annotation 
  3. https://support.10xgenomics.com/single-cell-vdj/software/overview/welcome 
  4. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/7.0/advanced/h5_matrices
  5. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/7.0/output/matrices
  6. https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/algorithms/annotation#productive
  7. https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/vdj 
  8. https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi