Question: Is it possible to aggregate different libraries after running
cellranger vdj? I want to visualize multiple TCR or BCR libraries in Loupe V(D)J Browser, similar to aggregating and visualizing multiple gene expression libraries in Loupe Cell Browser.
Answer: Starting from Cell Ranger version 5.0, it is possible to aggregate multiple V(D)J libraries through the
cellranger aggr pipeline, like you can for 3' and 5' gene expression libraries. When running the pipeline you need to specify the vdj_contig_info.pb output file from each
vdj run. It is also possible to add custom annotations for each run into
aggr, and these annotations can be viewed downstream in Loupe V(D)J browser. For more information, please refer to our support page.