10x Genomics
Chromium Single Cell CNV

Cell Ranger DNA1.1 (latest), printed on 11/23/2024

Understanding Output

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.

Output Files

Barcoded BAM files

Standards-compliant BAM files, with barcode information, for all reads, sorted by alignment position.

CNV BED files

Tab-separated text files containing copy number calls genome wide for every single cell and group of cells defined by the clustering, and a list of mappable genomic regions.

Summary CSV files

CSV files with sample metrics and per-cell summary metrics.

Run Summary HTML

This is a single page overview, mostly consisting of metrics regarding the experiment and some automated secondary analysis. You'll see topline results about the number of cells, mean reads per cell, read quality summaries, etc.

Read count, CNV, clustering data bundled in the HDF5 format

Matrices showing the raw and normalized read-pair counts for each chromosome and each cell (and group of cells), genome tracks with information about GC content and mappability, copy number calls across the genome for each cell (and group of cells), the hierarchical clustering, barcode sequences for all the cells, and a few useful sample metrics.

Loupe scDNA Browser file

Refer to the Loupe scDNA Browser page for more details.

Run alerts

A list of potential data issues caused by the library preparation workflow, the sequencing, or the algorithms.

More information about the contents of the pipeline output directory can be found in the Pipestance Structure page.