Cell Ranger5.0, printed on 11/05/2024
The Cell Ranger software strives to maintain compatibility with common analysis tools by using standard output file formats whenever possible. For example, the barcoded BAM files can be viewed in standard genome browsers such as IGV to verify assembly quality and other features. The Chromium-specific data, including cellular barcodes and UMIs, can be accessed via any third-party tools or scripts that can parse the additional elements utilized by Cell Ranger.
All pipelines produce all of their output in a single pipeline output directory, whose name depends on the pipeline:
HAWT7ADXX).--id argument is used.Output files will appear in the outs/ subdirectory within this pipeline output directory. For example, a typical cellranger vdj run may look like:
$ cd /home/jdoe/runs $ cellranger vdj --id=sample345 \ --reference=/opt/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0 \ --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \ --sample=mysample \ Martian Runtime - v4.0.2 Running preflight checks (please wait)... yyyy-mm-dd hh:mm:ss [runtime] (ready) ID.sample345.SC_VDJ_ASSEMBLER_CS.VDJ_PREFLIGHT yyyy-mm-dd hh:mm:ss [runtime] (run:local) ID.sample345.SC_VDJ_ASSEMBLER_CS.VDJ_PREFLIGHT.fork0.chnk0.main yyyy-mm-dd hh:mm:ss [runtime] (ready) ID.sample345.SC_VDJ_ASSEMBLER_CS.VDJ_PREFLIGHT_LOCAL ... Outputs: - Run summary HTML: /home/jdoe/runs/sample345/outs/web_summary.html - Run summary CSV: /home/jdoe/runs/sample345/outs/metrics_summary.csv - Clonotype info: /home/jdoe/runs/sample345/outs/clonotypes.csv - Filtered contig sequences FASTA: /home/jdoe/runs/sample345/outs/filtered_contig.fasta - Filtered contig sequences FASTQ: /home/jdoe/runs/sample345/outs/filtered_contig.fastq - Filtered contigs (CSV): /home/jdoe/runs/sample345/outs/filtered_contig_annotations.csv - All-contig FASTA: /home/jdoe/runs/sample345/outs/all_contig.fasta - All-contig FASTA index: /home/jdoe/runs/sample345/outs/all_contig.fasta.fai - All-contig FASTQ: /home/jdoe/runs/sample345/outs/all_contig.fastq - Read-contig alignments: /home/jdoe/runs/sample345/outs/all_contig.bam - Read-contig alignment index: /home/jdoe/runs/sample345/outs/all_contig.bam.bai - All contig annotations (JSON): /home/jdoe/runs/sample345/outs/all_contig_annotations.json - All contig annotations (BED): /home/jdoe/runs/sample345/outs/all_contig_annotations.bed - All contig annotations (CSV): /home/jdoe/runs/sample345/outs/all_contig_annotations.csv - Barcodes that are declared to be targetted cells: /home/jdoe/runs/sample345/outs/cell_barcodes.json - Clonotype consensus FASTA: /home/jdoe/runs/sample345/outs/consensus.fasta - Clonotype consensus FASTA index: /home/jdoe/runs/sample345/outs/consensus.fasta.fai - Contig-consensus alignments: /home/jdoe/runs/sample345/outs/consensus.bam - Contig-consensus alignment index: /home/jdoe/runs/sample345/outs/consensus.bam.bai - Clonotype consensus annotations (CSV): /home/jdoe/runs/sample345/outs/consensus_annotations.csv - Concatenated reference sequences: /home/jdoe/runs/sample345/outs/concat_ref.fasta - Concatenated reference index: /home/jdoe/runs/sample345/outs/concat_ref.fasta.fai - Contig-reference alignments: /home/jdoe/runs/sample345/outs/concat_ref.bam - Contig-reference alignment index: /home/jdoe/runs/sample345/outs/concat_ref.bam.bai - Loupe V(D)J Browser file: /home/jdoe/runs/sample345/outs/vloupe.vloupe - V(D)J reference: fasta: regions: /home/jdoe/runs/sample345/outs/vdj_reference/fasta/regions.fa donor_regions: /home/jdoe/runs/sample345/outs/vdj_reference/fasta/donor_regions.fa reference: /home/jdoe/runs/sample345/outs/vdj_reference/reference.json - AIRR Rearrangement TSV: /home/jdoe/runs/sample345/outs/airr_rearrangement.tsv - All contig info (ProtoBuf format): /home/jdoe/runs/sample345/outs/vdj_contig_info.pb Waiting 6 seconds for UI to do final refresh. Pipestance completed successfully!
In this case,
/home/jdoe/runs/ is where the pipeline was run,/home/jdoe/runs/sample345/ is the top-level output directory containing pipeline metadata, and/home/jdoe/runs/sample345/outs/ contains the final pipeline output files.The contents of this outs/ directory contain the data that is described in the remainder of this section:
cell_barcodes.json: This file lists the barcodes which are identified as T/B cells.vdj_contig_info.pb: This file stores the contig annotations, V(D)J reference and additional metadata in a protobuf binary file format. This file is required to run the cellranger aggr pipeline.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. 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.
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.