Cell Ranger2.2, printed on 04/18/2024
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 and molecular barcodes, 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 usedOutput 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-2.0.0 \ --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \ --sample=mysample \ Martian Runtime - v2.3.3 Running preflight checks (please wait)... 2016-01-01 10:23:52 [runtime] (ready) ID.sample345.SC_VDJ_ASSEMBLER_CS.SC_VDJ_ASSEMBLER.SETUP_CHUNKS ... 2017-04-15 14:32:18 [runtime] (join_complete) ID.sample345.SC_VDJ_ASSEMBLER_CS.VLOUPE_PREPROCESS Outputs: - Run summary HTML: /home/jdoe/runs/sample345/outs/web_summary.html - Run summary CSV: /home/jdoe/runs/sample345/outs/metrics_summary.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 - 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 - 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 - Concatenated reference sequences: /home/jdoe/runs/sample345/outs/concat_ref.fasta - Concatenated reference index: /home/jdoe/runs/sample345/outs/concat_ref.fasta.fai - Contig-consensus alignments: /home/jdoe/runs/sample345/outs/consensus.bam - Contig-consensus alignment index: /home/jdoe/runs/sample345/outs/consensus.bam.bai - Contig-reference alignments: /home/jdoe/runs/sample345/outs/concat_ref.bam - Contig-reference alignment index: /home/jdoe/runs/sample345/outs/concat_ref.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 - Clonotype info: /home/jdoe/runs/sample345/outs/clonotypes.csv - Loupe V(D)J Browser file: /home/jdoe/runs/sample345/outs/vloupe.vloupe 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:
More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.