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). What is the issue here?
Answer: The reason that you are seeing this warning is that there is less than the required (75% of smaller barcode count) overlap between the cell barcodes in your gene expression and VDJ data.
You can click the "continue loading VDJ" to view the VDJ data that contain overlapping barcodes with the gene expression data. However, you will not be able to view the data of the non-overlapping barcodes.
On the other hand, with the current version of Loupe VDJ Browser, you will not be able to load the gene expression data into the Loupe VDJ browser, when the overlap is less than 75%. For a workaround, you can run
cellranger reanalyze with the
--barcodes argument specifying the barcodes identified as cells in the VDJ assay. Then the newly generated
cloupe.cloupe should be able to load into the Loupe VDJ Browser.