Import Immune Reference Segments
The Import Immune Reference Segments tool can import reference sequences for V, D, J and C gene-segments from a fasta file. The sequences are needed when running Single Cell V(D)J-Seq Analysis (Single Cell V(D)J-Seq Analysis) for either T or B cell receptor repertoires (TCR and BCR, respectively).
The importer can be found here:
Import (
) | Import Immune Reference Segments (
).
The importer can be used to import fasta files that are either in the IMSEQ [Kuchenbecker et al., 2015] or IMGT [Lefranc et al., 2009] format (see figure 2.14).
Figure 2.14: The available options when importing immune reference segments.
Both formats support allele numbering for the gene segments. If Import only the first allele is ticked, only segments without an allele or those with an allele defined as the number "1" (i.e "01" is also valid) will be imported. Otherwise, all segments are imported.
The two formats differ in how the sequence header is parsed for identifying the gene segment and related information, and how the conserved amino acids in the V and J segments are identified.
When saving the results, the reference data for either TCR, or BCR, or both, can be saved. The wizard will show an error message if an output option is ticked for which no relevant reference sequences are available.
The importer can only handle one fasta file at a time, but if two or more fasta files are imported, the resulting sequence lists can subsequently be combined to one list using the Create Sequence List tool.
Subsections