How to add custom tracks in UCSC Browser?

Introduction to Custom Tracks

• The UCSC Genome Browser allows users to add custom tracks, which are custom annotations for genomic regions. This guide explains how to add these tracks effectively.

Prepare Your Data

• Ensure your data is in a compatible format, such as BED, GFF, or VCF. These formats describe genomic regions and annotations.
• Check for data integrity; malformed data might not be loaded correctly.

Access the UCSC Genome Browser

• Navigate to the official UCSC Genome Browser website.
• Select the genome assembly you are interested in, e.g., GRCh38/hg38 for human studies.

Open the Custom Tracks Page

• On the main browser page, find and click the "My Data" tab in the top menu.
• From the dropdown, select "Custom Tracks", which brings you to the custom track management page.

Enter or Upload Your Data

• Use the text box to enter your custom track data directly if it is small and manageable.
• Alternatively, use the "Choose File" button to upload a file containing your data.

Describe Your Custom Track

• Provide a name for your track with the 'track name' parameter. This helps in identifying it easily.
• Add any desired styling or configuration parameters such as colors, visibilities, and labels for better visualization.

Submit Your Custom Track

• After entering or uploading your data, click the “Submit” button to add the track to the UCSC Genome Browser.
• Successful submissions will generate a preview window showing how the track appears in the browser.

Verify the Custom Track

• Ensure that your custom track displays correctly. Navigate around the genome to check for expected positioning and styling.
• If any issues are present, return to the custom tracks page to edit and resubmit the data.

Save and Share Your Track

• To save your custom track for later use, click on the "Sessions" tab to create a session that you can reload.
• Share the session URL with collaborators to allow them to view your custom track.