Convert Clonotypes to Cell Annotations

The Convert Clonotypes to Cell Annotations tool can be found in the Toolbox here:

        Immune Repertoire (Image sc_immune_rept_folder_open_16_n_p) | Convert Clonotypes to Cell Annotations (Image convert_cell_clonotypes_to_cell_annotations_16_n_p)

The tool takes a TCR Cell Clonotypes (Image cell_tcr_clonotypes_16_n_p) or BCR Cell Clonotypes (Image cell_bcr_clonotypes_16_n_p) element as input and produces a single Cell Annotations (Image cell_annotations_16_n_p) element summarizing the clonotypes.

Note that the tool only includes the primary and secondary clonotypes for each barcode. The Cell Clonotypes created by the Single Cell V(D)J-Seq Analysis tool only contain primary / secondary clonotypes, but the Combine Cell Clonotypes tool can lead to barcodes containing more clonotypes.

The output contains multiple categories that summarize the primary and secondary clonotypes for each barcode. The cells can be colored by any of the available categories in a Dimensionality Reduction Plot (see Dimensionality reduction) obtained from matched scRNA-Seq data for the same cells (see figure 10.7).

The cells in the Dimensionality Reduction Plot and those in the Cell Annotations need to have the same sample name. Ideally, it should be ensured that these share the sample name as a first step in the analysis pipeline, when running the Annotate Reads with Cell and UMI tool (see Annotate Reads with Cell and UMI), or when importing the Cell Clonotypes element (see Import Cell Clonotypes). If this has not been done, the sample name can be updated using the Update to Common Sample Name tool (see Update to Common Sample Name).

Common to TCR Cell Clonotypes and BCR Cell Clonotypes is the 'Clone size' for each barcode: the number of barcodes it shares its primary clonotype with.

Note: The clone size reflects only the primary clonotypes. Let us consider the following example with TCR clonotypes, where each column represents one barcode, and the rows identify the TRA and TRB clonotypes by name:

  B1 B2 B3
Primary TRA clonotype TRA-1 TRA-2 TRA-1
Primary TRB clonotype TRB-1 TRB-2 None
Secondary TRA clonotype TRA-2 None None
Secondary TRB clonotype TRB-2 None None
Each barcode in this example has a clone size of one, because they are not sharing the primary TRA + TRB clonotypes with any other barcode, even though they have TRA and TRB clonotypes in common. To obtain the clone size for clonotypes other than the primary, the input Cell Clonotypes can be filtered first using the Filter Cell Clonotypes tool, see Filter Cell Clonotypes.

The remaining categories in the output Cell Annotations (Image cell_annotations_16_n_p) element are different for TCR Cell Clonotypes and BCR Cell Clonotypes.