Question: I am sure my .cloupe and .vloupe files are matched, but when I load the .vloupe file to Loupe Cell Browser, it says "The VDJ file may not be related to this gene expression dataset" (screenshot below). Why is this happening?
Answer: You see this warning because there is less than the required (40% of smaller barcode count) overlap between the cell barcodes in your gene expression and V(D)J data.
This issue may arise when you analyze gene expression and V(D)J datasets using different Cell Ranger pipelines (count and vdj, respectively). We now recommend using the cellranger multi pipeline (available in Cell Ranger 5+), which can simultaneously process 5' gene expression and V(D)J libraries from a single GEM well. The multi pipeline uses inferred cell calls from the gene expression library to improve cell calls in the V(D)J dataset.
If you wish to use your current data, click the "Continue Loading VDJ" button. It allows you to view V(D)J data that contain overlapping barcodes with the gene expression dataset. However, you cannot view non-overlapping barcodes. Please note, you will be unable to load gene expression data into the Loupe V(D)J Bowser with <75% barcode overlap. You must rerun the analysis with cellranger multi.