Filter Cell Clonotypes

Sometimes it can be desirable to restrict TCR Cell Clonotypes (Image cell_tcr_clonotypes_16_n_p) or BCR Cell Clonotypes (Image cell_bcr_clonotypes_16_n_p) to only a specific subset, for example only productive clonotypes, or only barcodes that are present in matched scRNA-Seq data. This can be achieved with the Filter Cell Clonotypes tool. Alternatively, the clonotypes can be filtered to a selection in the Cell Clonotypes tables (Cell Clonotypes tables) by using the option "Create Cell Clonotypes from Selection" from the right-click menu.

The Filter Cell Clonotypes tool can be found in the Toolbox here:

        Immune Repertoire (Image sc_immune_rept_folder_open_16_n_p) | Filter Cell Clonotypes (Image sc_cell_clonotypes_filter_16_n_p)

The tool takes a Cell Clonotypes element as input and produces a filtered element.

The following options can be adjusted (figure 10.4):

Image filter_clonotypes_wizard
Figure 10.4: The options in the dialog of the Filter Cell Clonotypes tool.

The options above can be mixed and matched to obtain the desired output. Note that the filters are applied in the order given above.

For example, assume we want to only use the primary productive TRB clonotypes. This can be obtained by setting "Productive status to retain" to "Productive", "Chains to retain" to "TRB", and "Multiple clonotypes" to "Retain primary". If one barcode A has a primary non-productive and a secondary productive TRB clonotype, the non-productive clonotype will be removed first and the productive one will become the primary one. Hence, "Retain primary" will have no effect on this barcode. If another barcode has two productive TRB clonotypes, "Retain primary" will remove the secondary clonotype.

If the desired behavior is that barcode A should be entirely removed from the output, as its primary clonotype is not productive, the tool can be run multiple times such that the filters are applied in a different order. By running the tool with "Multiple clonotypes" to "Retain primary" first, the barcode will have only the non-productive clonotype. A second execution of the tool with "Productive status to retain" set to "Productive" and "Chains to retain" set to "TRB" will entirely remove the barcode.

The Filter Cell Clonotypes tool can optionally produce a report for each sample found in the input element, summarizing the clonotypes left after filtering. The output report includes the same information as the report produced by the Single Cell V(D)J-Seq Analysis tool, minus the assembly and trimming summaries (see The report output from Single Cell V(D)J-Seq Analysis).

To obtain a report summarizing clonotypes across samples, see Compare Single Cell Immune Repertoires.