Question: I want to run Cell Ranger's V(D)J pipeline on an organism different from human or mouse. How can I create a compatible V(D)J reference?
Answer: Generating a Cell Ranger compatible reference for V(D)J pipeline requires a reference genome FASTA and corresponding gene annotations in GTF format for your organism. With these two files, you can use the
cellranger mkvdjref utility that comes with Cell Ranger to generate a compatible reference package.
If you want to generate the reference using IMGT database, you could use a script (fetch-imgt) that comes with Cell Ranger v2.1 (or higher) to fetch the data from IMGT and then run
cellranger mkvdjref to generate the reference.
Please see here for more details on building a Cell Ranger compatible reference for the V(D)J pipeline.