Import Cell Clonotypes
Several formats produced by Cell Ranger can be imported into a TCR Cell Clonotypes (
) or BCR Cell Clonotypes (
) element using the following importers:
- AIRR: Import Cell Clonotypes in AIRR Format (
).
- CSV contig: Import Cell Clonotypes in Cell Ranger Contig Format (
);
The importers can be found here:
Import (
) | Single Cell Data (
) | Import Cell Clonotypes (
)
Most options are common to both importers. The following options can be adjusted:
- AIRR rearrangements / Contig annotations. The input .tsv or .csv file, respectively, following the official Cell Ranger format.
- Reference segments (Optional). A reference data element downloaded from the Reference Data Manager (see Reference data management) containing the corresponding QIAGEN V, D, J and C genes. When supplied, the gene names in the input file will be mapped to those used in the provided element. This is important when comparing imported Cell Clonotypes with those produced by the CLC Single Cell Analysis Module, see Compare Single Cell Immune Repertoires.
- Cell format and Sample. How cells are identified, see Cell format in importers for more details.
- Matrix (Optional). The sample name will be obtained from the supplied matrix. The importer does not check that the barcodes present in the input file match those in the matrix. If the matrix contains multiple samples, the importer will fail with a relevant message.
|
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.