Question: I would like to remove a group of cells from my sample using the Loupe Cell Browser software. I tried to use the lasso tool but I can't directly remove these cells from the analysis. So I would like to know if it is possible, and if yes, can you please tell me how to do it?
Answer: The easiest way to exclude a group of cells from your analysis is to use Loupe Cell Browser and cellranger reanalyze. Cell Ranger will then re-run PCA, t-SNE, clustering, and differential expression analyses using only the subset of barcodes that you selected with the lasso tool, and generate a new .cloupe file.
We'll use the AML tutorial that comes pre-bundled as an example. First, use the lasso tool to select all the cells you want to include in your downstream analysis - excluding the cells you don't want.
Next, assign your 'ingroup' cells to a new category/cluster (in this example, ingroup1), then export this to a CSV file using the option on the right side of the screen:
Loupe Cell Browser will then ask you if you want to include or exclude the unlabeled cells:
To export only the filtered cells, select 'Exclude Unlabeled'.
You can then supply the cellular barcodes in this CSV file into the --barcodes option of cellranger reanalyze which is documented on this page.
For more examples of how to select subsets of cells by manual selection or gene expression filtering, please see the Loupe Cell Browser Tutorial.