Import Cell Clonotypes

Several formats produced by Cell Ranger can be imported into a TCR Cell Clonotypes (Image cell_tcr_clonotypes_16_n_p) or BCR Cell Clonotypes (Image cell_bcr_clonotypes_16_n_p) element using the following importers:

The importers can be found here:

        Import (Image Next_Folder_16_n_p) | Single Cell Data (Image single_cell_importers_16_n_p) | Import Cell Clonotypes (Image import_cell_clonotypes_16_n_p)

Most options are common to both importers. The following options can be adjusted:

If sample name is not defined through either Cell format, Sample, or Matrix, the importer sets the sample name to the name of the input file. The sample name can be set using only one of these three options.

When matched scRNA-Seq data is available, it is important that the Cell Clonotypes and corresponding Expression Matrix/Dimensionality Reduction Plot have the same sample name, see Convert Clonotypes to Cell Annotations.

Note that the productive status is calculated from the CDR3 amino acid sequence found in the input file.