The Cell Ranger ATAC 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 alignment quality and other features. The Chromium-specific data, including these barcodes, can be accessed via any third-party tools or scripts that can parse the additional element tags utilized by Cell Ranger ATAC.

All pipelines produce all of their output in a single pipeline output directory, whose name depends on the pipeline:

• For cellranger-atac mkfastq, the flow cell serial number is used (e.g., HAWT7ADXX)
• For cellranger-atac count, the --id argument is used

Output files will appear in the outs/ subdirectory within this pipeline output directory. For example, a typical cellranger-atac count run may look like:

Copy
$ cd /home/jdoe/runs
$ cellranger-atac count --id=sample345 \
                 --reference=/opt/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 \
                 --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \
                 --sample=mysample


Martian Runtime - 4.0.7

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Outputs:
- Per-barcode fragment counts & metrics:        /home/jdoe/runs/sample345/outs/singlecell.csv
- Position sorted BAM file:                     /home/jdoe/runs/sample345/outs/possorted_bam.bam
- Position sorted BAM index:                    /home/jdoe/runs/sample345/outs/possorted_bam.bam.bai
- Summary of all data metrics:                  /home/jdoe/runs/sample345/outs/summary.json
- HTML file summarizing data & analysis:        /home/jdoe/runs/sample345/outs/web_summary.html
- Bed file of all called peak locations:        /home/jdoe/runs/sample345/outs/peaks.bed
- Smoothed transposition site track:            /home/jdoe/runs/sample345/outs/cut_sites.bigwig
- Raw peak barcode matrix in hdf5 format:       /home/jdoe/runs/sample345/outs/raw_peak_bc_matrix.h5
- Raw peak barcode matrix in mex format:        /home/jdoe/runs/sample345/outs/raw_peak_bc_matrix
- Directory of analysis files:                  /home/jdoe/runs/sample345/outs/analysis
- Filtered peak barcode matrix in hdf5 format:  /home/jdoe/runs/sample345/outs/filtered_peak_bc_matrix.h5
- Filtered peak barcode matrix in mex format:   /home/jdoe/runs/sample345/outs/filtered_peak_bc_matrix
- Barcoded and aligned fragment file:           /home/jdoe/runs/sample345/outs/fragments.tsv.gz
- Fragment file index:                          /home/jdoe/runs/sample345/outs/fragments.tsv.gz.tbi
- Filtered tf barcode matrix in hdf5 format:    /home/jdoe/runs/sample345/outs/filtered_tf_bc_matrix.h5
- Filtered tf barcode matrix in mex format:     /home/jdoe/runs/sample345/outs/filtered_tf_bc_matrix
- Loupe Browser input file:                     /home/jdoe/runs/sample345/outs/cloupe.cloupe
- csv summarizing important metrics and values: /home/jdoe/runs/sample345/outs/summary.csv
- Annotation of peaks with genes:               /home/jdoe/runs/sample345/outs/peak_annotation.tsv
- Peak-motif associations:                      /home/jdoe/runs/sample345/outs/peak_motif_mapping.bed

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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:

• Web Summary HTML
• Secondary Analysis
• Feature-barcode Matrices MEX
• HDF5
• Per Barcode QC, ATAC Signal, and Cell Calling
• Barcoded BAMs
• Fragments TSV
• Peaks BED
• Summary Metrics
• Peak Annotations

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