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: You are seeing this warning because there is less than the required (40% of smaller barcode count) overlap between the cell barcodes in your gene expression and VDJ data.
When you encounter this issue, most likely, you have analyzed the Gene Expression and VDJ data separately using
cellranger count and
cellranger vdj pipelines. We now recommend using
cellranger multi pipeline (available in Cell Ranger 5+), which can simultaneously process 5' Gene Expression and VDJ libraries from a single GEM well. The multi pipeline uses the cell calls from gene expression data to improve the cell calls inferred by the VDJ library.
If you still want to use the current 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, in 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%. You will need to rerun the analysis with
cellranger multi pipeline.