Question: I have a cloupe file generated from multiple samples using cellranger aggr. How can I create clusters of a specific cell type in different samples?
Answer: You will need Loupe Cell Browser 3.1 (or higher) to be able to use the instructions below. In this example, we will use the AMLTutorial dataset bundled with Loupe Cell Browser installation.
The cloupe file generated by cellranger aggr contains a category called LibraryID that clusters cells based on libraries/samples. In this AMLTutorial dataset, there are 3 libraries: AMLNormal1, AMLNormal2 and AMLPatient
For the purpose of this instruction, let us identify B cells in each sample.
(1) First, let us create a new category with a B-cell cluster based on our marker genes. Below GIF demonstrates the process
(2) Now we can use the Filters to create a new category with three clusters of B cells (one cluster for each library). Below GIF demonstrates the process
At the end of the process, you should have 3 clusters of B cells, one for each library: 