dd6958bf3e8dfeb13dad8906a5c471293c471152
mspeir
  Wed Jul 22 07:56:17 2026 -0700
Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box

Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with
the current genome search box, re-recorded the step GIFs, and expanded the
guided walkthroughs (Table Browser filter/intersection and output fields,
Custom Track track line, Gateway GenArk/recent-genomes and species tree).

refs #37355

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

diff --git docs/tutorials/customTrackTutorial.md docs/tutorials/customTrackTutorial.md
index 5ebb1da425f..cc0853af9e0 100644
--- docs/tutorials/customTrackTutorial.md
+++ docs/tutorials/customTrackTutorial.md
@@ -62,35 +62,33 @@
 <h6>Manage Custom Tracks</h6>
 ``` image
 src=/images/tutorialImages/hgCustomAnnotated_pt2.png
 width=65%
 ```
 
 ---
 
 ## Guided Walkthrough
 
 
 <div class="row">
   <div class="col-md-6">
 ### 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)
+  Use the **Change selected genome** search box to switch assemblies. Type a species name, common
+  name, or assembly ID, then choose one from the list. **Current Genome** shows which assembly is
+  active.
   </div>
 
   <div class="col-md-6">
   ```image
   src=/images/tutorialImages/gif/hgCustomStep1.gif
   width=90%
   ```
 </div>
 </div>
 
 ---
 
 
 <div class="row">
   <div class="col-md-6">
@@ -104,30 +102,50 @@
 ### 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)
   </div>
 </div>
 
 ---
 
+### The track line
+
+Along with the browser line, a **track line** sits above your data and sets what the track is
+called and how it looks. It is optional for a quick look, but worth adding if you plan to keep
+or share the track. Common attributes:
+
+- `name` — the short label shown to the left of the track
+- `description` — the longer text shown in the track's title and details page
+- `visibility` — how the track is drawn: `hide`, `dense`, `squish`, `pack`, or `full`
+- `color` — the feature color as RGB values, for example `color=0,0,255` for blue
+
+A track line looks like:
+
+    track name="My variants" description="Sample calls" visibility=pack color=0,0,255
+
+For bigBed, bigWig, bigGenePred, CRAM, BAM, and VCF files you can skip the track line and
+paste just the URL to the file, one per line.
+
+---
+
 
 <div class="row">
   <div class="col-md-6">
 ### 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.