Question: I am analyzing a .cloupe file that resulted from running cellranger aggr on two separate libraries. Is there a way in Loupe Browser to view these two libraries separately?
Answer: Yes, using the pre-bundled AML tutorial dataset as an example, which was also created using cellranger aggr on three libraries, you can select "LibraryID" from the drop-down menu on the top right:
The LibraryID names correspond to the first column of the CSV file that you input to cellranger aggr as described on this page.
You will now notice the t-SNE plot is colored according to LibraryID. You can click "Split on Category" and select "LibraryID" to view them separately:
You can now compare these clusters (e.g. using Significant Genes) just as you would for any other clusters.