10x Genomics
Chromium Single Cell ATAC

Cell Ranger ATAC3.0, printed on 12/22/2024

Loupe Cell Browser ATAC Tutorial

Welcome to the Loupe Cell Browser ATAC tutorial. In the next few pages, we will be finding significant features, analyzing differential accessibility patterns, and exploring substructure within a real-world dataset. Along the way, we'll touch on most of the features of Loupe Cell Browser.

Setup

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

You can also access the tutorial dataset by clicking on 'Load ATAC Tutorial Dataset' from the Help menu.

Now that you've loaded the file and familiarized yourself 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 targeted cell count was 5,000 and the observed barcode count from the pipeline was 5,335.