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: We do not currently offer a pipeline to aggregate V(D)J libraries like you can with
cellranger aggr for 3' and 5' gene expression libraries. However, there is a work-around to combine V(D)J libraries. Cell Ranger uses a pipeline management framework called Martian. The pipeline and each stage in it is specified by a configuration file called an MRO file. Usually, the cellranger commands create the appropriate MRO files for you, but in the case that you want to do something outside the normal workflows, it is possible to create a custom MRO file to directly exercise the full range of features. For more information please see Running Multi-Library Samples.