10x Genomics
Chromium Single Cell ATAC
Cell Ranger ATAC6.1, printed on 12/22/2024
Loupe Browser ATAC Tutorial
Welcome to the Loupe Browser ATAC tutorial. In the next few pages, we will find significant features, analyze differential accessibility patterns, and explore substructure within a real-world dataset. Along the way, we will touch on most of the features of Loupe Browser.
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.
