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Cell Ranger


10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger Integration

The cellranger vdj pipeline will generate .vloupe files for Single Cell V(D)J experiments. A .vloupe file will be found in the outs folder of a completed cellranger vdj run.

Note that the .vloupe files are not compatible with all versions of Loupe V(D)J Browser and Loupe Browser. Loupe V(D)J Browser version 4.0 and Loupe Browser version 5.0 only support .vloupe files generated by Cell Ranger version 5.0 and above. To view .vloupe files from Cell Ranger version 4.0 or below you will need to use Loupe V(D)J Browser version 3.0 and Loupe Browser version 4.2 or below.

Information Exclusive to the Web Summary View

You will still need to consult the Cell Ranger run summary file to view quality control data and other metadata about a particular run; this is not yet available in Loupe V(D)J Browser.

Cell Ranger 3.0 and later generates a .cloupe file for multi-species ("barnyard") experiments run with a joint reference. This allows Loupe Browser to compute an aggregate transcriptome expression count per cell, enabling easy segmentation by species, or joint analysis for host-virus applications. Please note that barnyard experiments are for 5’ single cell gene expression data only, not 5' single cell V(D)J.