10x Genomics
Chromium Single Cell ATAC

Cell Ranger ATAC6.3, printed on 12/22/2024

Loupe Browser ATAC Tutorial

The Loupe Browser ATAC tutorial demonstrates how to find significant features, analyze differential accessibility patterns, and explore substructure within a real-world dataset.

• Navigation
• Identifying Cell Types
• Identifying Cell Subtypes
• Peak Viewer
• Significant Features
• Sharing Results
• Interoperability

Setup

Before beginning the tutorial, make sure you have downloaded Loupe Browser. If this is your first time working with Loupe Browser, you can access the ATAC tutorial dataset by clicking on the ATACTutorial.cloupe link on the Recent Files page as seen below.

Once the file is loaded and you are familiar with some ATAC data concepts, click here to tour the user interface.

About the ATAC tutorial dataset

The ATAC tutorial dataset contains the results of a cellranger-atac run over a set of human peripheral blood mononuclear cells, with the standard Chromium™ Single Cell ATAC protocol.

The key metrics include:

• Targeted cell count - 5,000
• Observed barcode count from the pipeline - 5,335

Sharing usage data

Starting with Loupe Browser v6.1, users may choose to share anonymized non-biological usage data (i.e. no identifiable sample information such as files, cluster names, or any open text fields are tracked) to improve Loupe Browser performance. Sharing of usage data is optional, and users can change whether they want to share usage data any time. The user preference for usage data sharing will carry over within a major version (e.g. all 6.Y versions) but the user will be asked to confirm their preferences for each major version update.

In case you wish to change usage data sharing setting, click the Manage Usage Data from the Help menu and change the preference in the pop-up window.