Cell Ranger4.0, printed on 12/26/2024
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-4.0.0 \ --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \ --sample=mysample \ Martian Runtime - v4.0.0 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 - Clonotype consensus FASTQ: /home/jdoe/runs/sample345/outs/consensus.fastq - 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 (JSON): /home/jdoe/runs/sample345/outs/consensus_annotations.json - 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 reference: /home/jdoe/runs/sample345/outs/vdj_reference/reference.json - AIRR Rearrangement TSV: /home/jdoe/runs/sample345/outs/airr_rearrangement.tsv 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:
In addition, there is a file cell_barcodes.json that lists the barcodes which are
identified as targeted cells.
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.
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.
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.