10x Genomics Support/Cell Ranger 7.2/Analysis/

Cell Ranger vdj Outputs

This page describes the cellranger vdj output file structure for 5' Chromium Next GEM Single Cell V(D)J data. Refer to the cellranger vdj pipeline page or work though the vdj tutorial to learn about running cellranger vdj.

For any given cellranger vdj run, the output folder name is the same as the run ID specified during the run (HumanB_Cell/ in this example). The outs/ subfolder contains the main pipeline outputs:

── runs └── HumanB_Cell ├── outs ├── airr_rearrangement.tsv ├── all_contig_annotations.bed ├── all_contig_annotations.csv ├── all_contig_annotations.json ├── all_contig.bam ├── all_contig.bam.bai ├── all_contig.fasta ├── all_contig.fasta.fai ├── all_contig.fastq ├── cell_barcodes.json ├── clonotypes.csv ├── concat_ref.bam ├── concat_ref.bam.bai ├── concat_ref.fasta ├── concat_ref.fasta.fai ├── consensus_annotations.csv ├── consensus.bam ├── consensus.bam.bai ├── consensus.fasta ├── consensus.fasta.fai ├── filtered_contig_annotations.csv ├── filtered_contig.fasta ├── filtered_contig.fastq ├── metrics_summary.csv ├── vdj_contig_info.pb ├── vdj_reference ├── vloupe.vloupe └── web_summary.html
NameDescription
web_summary.htmlRun summary metrics and charts in HTML format, described in the Web Summary page.
metrics_summary.csvRun summary metrics file in CSV format, described in the Metrics page.
vdj_referenceA copy of the V(D)J reference transcriptome supplied as an input to the run.
vloupe.vloupeLoupe V(D)J Browser readable file.
vdj_contig_info.pbStores contig annotations, V(D)J reference, and additional metadata in a protobuf binary file format. Required file to run the cellranger aggr pipeline. This file is only meant to serve as an input to the Cell Ranger aggr pipeline and must not be used as a source of data. Information contained in the vdj_contig_info.pb is also available in other, easy-to-parse output files like all_contig_annotations.json, vdj_reference, and metrics_summary.csv.
cell_barcodes.jsonList of barcodes identified as T/B cells.
clonotypes.csvHigh-level description of each clonotype.
FASTA & FASTQ filesFASTA, indexed FASTA, and FASTQ files, as described on the FASTA/FASTQ page:
all_contig.fasta
all_contig.fasta.fai
all_contig.fastq
consensus.fasta
consensus.fasta.fai
concat_ref.fasta
concat_ref.fasta.fai
filtered_contig.fasta
filtered_contig.fastq
Annotation filesAmino acid and nucleotide sequences for framework and complementarity determining regions (CDRs). Described on the Annotations page:
airr_rearrangement.tsv
all_contig_annotations.bed
all_contig_annotations.json
consensus_annotations.csv
filtered_contig_annotations.csv
BAM filesBAM files for use with BAM visualization tools (e.g. Integrated Genome Viewer):
all_contig.bam
all_contig.bam.bai
concat_ref.bam
concat_ref.bam.bai
consensus.bam
consensus.bam.bai

More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.

Cell Ranger vdj web summary

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

The .vloupe files are not compatible with all versions of Loupe V(D)J Browser and Loupe Browser. Loupe V(D)J Browser v4.0 and Loupe Browser v5.0 only support .vloupe files generated by Cell Ranger v5.0 and later. To view .vloupe files from Cell Ranger v4.0 or earlier you must use Loupe V(D)J Browser v3.0 and Loupe Browser v4.2 or earlier.