Question: Can we use the
cellranger vdj pipeline on organisms that do not have a reference genome?
Answer: Yes. The
cellranger vdj pipeline will work with organisms that do not have a reference genome or have a reference genome with poorly annotated V(D)J genes. In these cases, you can use the
--denovo mode to turn off the reference specific stages (read filtering and V(D)J annotation).
When run in
--denovo mode, the pipeline will still assemble contigs de novo. When running in
.vloupe files for importing the data to Loupe V(D)J Browser are not generated. Please see this page for more details.