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Cell Ranger


10x Genomics
Chromium Single Cell Immune Profiling

Understanding Cell Ranger V(D)J Output

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

Output file descriptions

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 files FASTA, 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 files Amino 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 files BAM 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.

Loupe Integration

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.

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.