Cell Ranger7.1, printed on 11/05/2024
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
| Name | Description |
|---|---|
web_summary.html | Run summary metrics and charts in HTML format, described in the Web Summary page. |
metrics_summary.csv | Run summary metrics file in CSV format, described in the Metrics page. |
vdj_reference | A copy of the V(D)J reference transcriptome supplied as an input to the run. |
vloupe.vloupe | Loupe V(D)J Browser readable file. |
vdj_contig_info.pb | Stores 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.json | List of barcodes identified as T/B cells. |
clonotypes.csv | High-level description of each clonotype. |
FASTA & FASTQ files | FASTA, indexed FASTA, and FASTQ files, as described on the FASTA/FASTQ page:
|
Annotation files | Amino acid and nucleotide sequences for framework and complementarity determining regions (CDRs). Described on the Annotations page:
|
BAM files | BAM files for use with BAM visualization tools (e.g. Integrated Genome Viewer):
|
More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.
The cellranger vdj pipeline will generate .vloupe files for Single Cell
V(D)J experiments. The .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.
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.