Question: Are there any cell types that express transcripts that are not fully recombined for VDJ?
Answer: Yes, there are some cell types for both B and T cells where you can see incomplete recombination. When this occurs, you will get recombination of the C and J genes but no V gene present.
You will not see these events in V(D)J Loupe Browser, as these transcripts are not productive. The contigs are however present in the fasta file (raw) output by Cellranger - but further downstream analysis may be required to get evidence of this incomplete recombination.
Products: Single Cell Immune Profiling