10x Genomics Support/Loupe Browser/Analysis/

Loupe Browser ATAC Tutorial

Loupe Browser 7.0 introduces an enhanced user interface (UI). Visit the navigation tutorial available on our new support website for a comprehensive understanding of these UI improvements.

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

Before beginning the tutorial, 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.

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