Question: How can I create categories in the .cloupe file starting from cellranger aggr?
Answer: When setting up an aggregation CSV for cellranger aggr, columns representing library-based categories can be added along with the required columns for the library_id and molecule_h5 path. Along with library_id, the additional categories will be included in the .cloupe file for Loupe Cell Browser.
library_id,molecule_h5,patient DS123,/opt/runs/DS123/outs/molecule_info.h5,disease DS456,/opt/runs/DS456/outs/molecule_info.h5,disease NOP789,/opt/runs/NOP789/outs/molecule_info.h5,normal
For more information please see Multi-Library Aggregation.