Question: Is it possible to aggregate different libraries after running cellranger vdjor multi? 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: With Cell Ranger v5.0+, it is possible to aggregate multiple V(D)J libraries using the cellranger aggr pipeline, like you would for 3' and 5' gene expression libraries. When running the pipeline you must specify the vdj_contig_info.pb output file from each cellranger
vdj or multi run. It is also possible to add custom annotations for each run into cellranger
aggr, and these annotations can be viewed downstream in Loupe V(D)J browser. For more information, please refer to our support page.
Note: Individual cellranger vdjruns were possible to be used in comparison mode on Loupe V(D)J Browser if it was run on Cell Ranger v4.0 or earlier and viewed on Loupe V(D)J Browser v3 and earlier. This function has been disabled with the launch of cellranger
aggr on vdj and multi in the newer releases of Cell Ranger, where it is no longer required to use comparison mode; instead one can view the aggregated .vloupe file on the latest version of Loupe V(D)J Browser.
Products: Single Cell Immune Profiling