Question: What is the difference between the gene expression (GEX) and V(D)J reference packages - can we use one instead of the other?
Answer: No. The gene expression and V(D)J references are completely different reference packages and cannot be interchanged.
The gene expression reference packages for human and mouse represent the whole transcriptome for these organisms and are used for 5' and 3' single cell gene expression analysis with the cellranger count pipeline. The reference packages can be downloaded here.
The V(D)J references (for human and mouse) consist of only V(D)J-specific genes and annotations for each organism in a 10x specific format for the cellranger vdj pipeline. The reference packages can be downloaded here.
Products: Single Cell Gene Expression, Single Cell Immune Profiling