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: To generate a Cell Ranger compatible reference for the V(D)J pipeline using the Ensembl database, you will need the reference genome FASTA and its corresponding gene annotations in GTF format for your organism. Then, you can run the Cell Ranger's cellranger mkvdjref utility to generate a compatible reference package.
To generate your reference using the IMGT database, use the fetch-imgt script provided with Cell Ranger v2.1+ to fetch the data from IMGT. Then run cellranger mkvdjrefto generate the reference.
Click here for more details on building a Cell Ranger compatible reference for the V(D)J pipeline. Also see a related KB article on building a custom reference for V(D)J using IMGT tool.
Note: Currently, in Cloud platform we do not support running Cell Ranger V(D)J in de novo mode without a reference. We are planning to add support for this option in Cloud in a future release. De novo mode without a reference is enabled in cellranger command line.
Related Article: Usage of Cell Ranger VDJ denovo mode
Product: Single Cell Immune Profiling