Cell Ranger DNA1.1 (latest), printed on 05/29/2020
The Cell Ranger DNA software strives to maintain compatibility with common third-party 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 alignment 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 DNA.
All pipelines produce all of their output in a single pipeline output directory, whose name is determined by the --id argument. Output files will appear in the outs/ subdirectory within this pipeline output directory. For example, a typical
cellranger-dna cnv may look like:
$ cd /home/jdoe/runs $ cellranger-dna cnv --id=sample345 \ --reference=/opt/refdata-GRCh38-1.0.0 \ --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path Copyright (c) 2018 10x Genomics, Inc. All rights reserved. -------------------------------------------------------------------------------
Martian Runtime - 3.2.1 Running preflight checks (please wait)... 2018-04-19 10:26:05 [runtime] (ready) ID.sample345.CNV_CALLER_SINGLECELL_CS.CNV_CALLER_SINGLECELL._ALIGNER.SETUP_CHUNKS ... 2018-04-19 10:38:24 [runtime] (join_complete) ID.sample345.CNV_CALLER_SINGLECELL_CS.CNV_CALLER_SINGLECELL.DLOUPE_PREPROCESS
Outputs: - Position-sorted BAM: /home/jdoe/runs/sample345/outs/possorted_bam.bam - Position-sorted BAM index: /home/jdoe/runs/sample345/outs/possorted_bam.bam.bai - CNV calls with imputation: /home/jdoe/runs/sample345/outs/node_cnv_calls.bed - CNV calls without imputation: /home/jdoe/runs/sample345/outs/node_unmerged_cnv_calls.bed - Highly mappable regions: /home/jdoe/runs/sample345/outs/mappable_regions.bed - Per-cell summary metrics: /home/jdoe/runs/sample345/outs/per_cell_summary_metrics.csv - Analysis summary metrics: /home/jdoe/runs/sample345/outs/summary.csv - Run summary HTML: /home/jdoe/runs/sample345/outs/web_summary.html - HDF5 file with CNV data: /home/jdoe/runs/sample345/outs/cnv_data.h5 - Loupe visualization file: /home/jdoe/runs/sample345/outs/dloupe.dloupe - Run alerts: /home/jdoe/runs/sample345/outs/alarms_summary.txt 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.
More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.