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?
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: