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# 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.

## Keeping .vloupe and all_contig.bam Files Together

The .vloupe file contains information about clonotypes and consensus alignments, but does not contain the contig BAM file necessary to validate read support with the integrated IGV.js viewer. If the all_contig.bam file is not present in the same folder as the .vloupe file, you will be prompted to enter either its location on a filesystem, or a web address where the file can be found. If you are interested in validating read support, it may be worth it to keep the .vloupe and all_contig.bam files in the same folder, though the all_contig.bam file can grow very large.

## 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.