3724caa503e2454ffd577edc5a173279924107f5
jnavarr5
Fri Jan 30 15:51:30 2026 -0800
Staging the custom track markdown tutorial, refs #34354
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+% UCSC Genome Browser Custom Track Tutorial
+
+The UCSC Genome Browser allows users to load their own annoations by adding
+[Custom Tracks](../cgi-bin/hgCustom). Custom tracks work well for quickly displaying data and are
+automatically discarded 48 hours after the last time they were accessed.
+
+This tutorial introduces the Custom Track interface and demonstrates how to:
+
+- Select a genome and assembly
+- Define a region of interest
+- Format the custom track
+- Load a custom track into the Genome Browser
+- Manage custom tracks
+
+## Learning materials
+
+
+
+
+
Custom Track Overview
+
+A screenshot highlighting the layout and key elements of the Custom Track interface.
+
+
+
+
+
+
+
+
+
+
Guided Walkthrough
+
+Step-by-step guidance for using the Custom Track interface to upload data for your analysis.
+
+
+
+
+
+
+
+
+
+
Interactive Tutorial
+
+An in-browser walkthrough that introduces the Custom Track interface and workflow.
+
+
+### Step 1: Select Your Assembly
+
+ Use the **Clade**, **Genome**, and **Assembly** menus to choose your reference genome.
+
+ - *Clade*: Major organism group (e.g., Mammal, Vertebrate)
+ - *Genome*: Species (e.g., Human, Mouse)
+ - *Assembly*: Specific genome version (e.g., hg38)
+
+### Step 2: Create a browser line
+ The [browser line](/goldenPath/help/customTrack.html#BROWSER) controls where you are first taken
+ after uploading the custom track. This step controls the aspects of the overall display window.
+
+ For example, if the browser line `browser position chr22:1-20000` is used,
+ the Genome Browser window will initially display the first 20,000 bases of chromosome 22.
+
+ Browser lines are in the format:
+
+ browser attribute_name attribute_value(s)
+
+
+
+---
+
+
+
+
+### Step 3: Format the Data
+
+ The annotation data must be formatted into one of the [supporting formats](/FAQ/FAQformat.html).
+ For many formats, chromosome names can either be UCSC-style names (e.g. 'chr1', 'chrX') or
+ [aliases](/FAQ/FAQcustom.html#custom12) from other sources (e.g. '1' or 'NC\_000001.11').
+
+ While most data types can be uploaded directly to UCSC, any of the binary-indexed files
+ must be hosted on an external server. This includes formats such as bigBed, bigWig, BAM, VCF,
+ and other big\* files.
+
+ A few hosting resources that we recommend can be found on the
+ [Hosting](/goldenPath/help/hgTrackHubHelp.html#Hosting) help page.
+
+
+### Step 4: Load the custom track
+ Once the Browser and track lines are created, you can upload the custom track to the UCSC
+ Genome Browser using the dialogue box or the upload button to upload the custom track file.
+
+ When using a custom track file, you can also paste the URL to the custom track to quickly load
+ your annotations.
+
+ We recommend adding documentation to your custom annotation tracks, especially if you intend
+ to share the annotations with other collaborators.
+
+
+
+
+---
+
+
+
+### Step 5: Manage custom tracks page
+ Click to upload the data to the UCSC Genome Browser. You will be taken
+ to a new page where you can view all your uploaded custom tracks. Here, you can edit the
+ annotation data, or remove any custom tracks.
+
+ There is also a drop-down menu to view the data in other tools, such as:
+
+ - Genome Browser
+ - Table Browser
+ - Data Integrator
+ - Variant Annotation Integrator
+
+ Clicking on the chromosome hyperlink, e.g. chr21, in the table will take you to the Genome
+ Browser image to view the data.
+
+