10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger6.1, printed on 11/21/2024

Outputs Overview

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 their outputs in a single pipeline output directory, whose name depends on the pipeline:

• For cellranger mkfastq, the flowcell serial number is used (for example, HAWT7ADXX).
• For cellranger vdj, cellranger multi, cellranger count and cellranger aggr, the --id argument is used.

Output files will appear in the outs/ subdirectory within this pipeline output directory. Refer to the Understanding Outputs pages for more information on outs/ directory contents:

• cellranger multi outputs
• cellranger vdj outputs
• cellranger count outputs