0a6c6ae0e873e8c95fc1d6a941a26b50d7e92f36
mspeir
Wed Sep 16 11:40:45 2026 -0700
Add a blank line after the horizontal rules in the gb101 and gateway tutorials, no Redmine
These two pages put a bare --- rule directly above the next heading or div.
Pandoc reads a line of dashes as either a horizontal rule or a table rule
depending on what follows it, so the parse can flip when the block underneath
changes. It resolves to a rule today, but converting the divs on these pages to
fenced divs was enough to turn 5 sections of gb101 into tables and drop every
. The blank line removes the ambiguity. The built HTML is byte-identical
before and after.
Co-Authored-By: Claude Opus 5 (1M context)
diff --git docs/tutorials/gatewayTutorial.md docs/tutorials/gatewayTutorial.md
index a851fe2aafe..766c3ea011d 100644
--- docs/tutorials/gatewayTutorial.md
+++ docs/tutorials/gatewayTutorial.md
@@ -1,304 +1,306 @@
% UCSC Genome Browser Gateway Tutorial
The [UCSC Genome Browser Gateway](/cgi-bin/hgGateway) page is a tool for finding and accessing
genome assemblies. It features two search boxes: one for selecting an assembly and another for
specifying a genomic position. This tutorial will guide you through various features of the
Gateway page, including:
- Finding a genome browser using the Popular Species option
- Exploring the UCSC Species Tree
- Searching for an assembly using different identifiers
- Viewing sequences
- Using search terms to jump to a specific genome location
## Learning materials
Gateway Page Screenshot
A Gateway page screenshot highlighting its main features and functionalities.
Guided Walkthrough
A guided walkthrough that explains how to find a genome, explore the Species Tree, search with
assembly identifiers, view sequences, and use search terms to jump to genome locations.
Interactive Tutorial
An interactive tutorial that covers the basic Browser introduction on the Gateway page.
## Gateway page screenshot
```image
src=/images/tutorialImages/gatewayPageAnnotated.png
width=90%
```
## Guided Walkthrough
### Using the Popular Species Option
The **Popular Species** section lists commonly used model organisms, allowing for quick selection of
their genome browsers. Clicking on a species will display the default assembly version for that
organism.
---
+
NCBI
defines an assembly or assembled genome as the set of chromosomes, unlocalized and
unplaced (sometimes called "random") and alternate sequences used to represent an
organism's genome. The
NCBI Assembly Data Model defines assemblies as comprising one or more
assembly units.
The different assemblies often differ in their sequence content, with newer versions using newer
technologies to fill in gaps, correct errors, and refine genome structure. Some regions of an older
assembly may shift or change, while sequencing errors from previous data may be corrected in an
updated version. For example, the updated reference genome hg38 contains many improvements over the
hg19 assembly, some of which may include contigs that were merged together or placed where there
were previously sequence gaps.
To change the assembly version, click the **Assembly** option under **Find Position**.
The search box allows users to find genome assemblies by entering different types of queries:
Searching by **species name**: Ovis aries
Searching by **common name**: dog
Searching by **GC accession number**: GCF_016699485.2
Results are grouped by source. Assemblies listed under **UCSC Genome Browser assemblies** are
the long-standing browsers with tracks curated by UCSC. Those under **UCSC GenArk** come from
NCBI GenBank and RefSeq and are served as assembly hubs. There are hundreds of thousands of
GenArk assemblies, which is why the search box, rather than the species tree, is now the way
to reach most genomes.
The phylogenetic species tree is no longer shown by default; the **Browse/Select Species** column
now lists your **Recent Genomes** instead. Click **Show species tree** to display the tree. You can
scroll it or click different parts to move around, and hovering over a branch reveals the lineage
branch name.
**Note**: The Species Tree does not include all available Genome Browser assemblies. The process of
adding Genome Browsers has been streamlined, enabling rapid releases but omitting certain previous
features, such as inclusion in the Species Tree. To find a specific assembly, use the assembly
search box.
---
### Requesting an Assembly
If a desired assembly is not listed, you can request it by clicking **"Unable to find a
genome? Send us a request**". This will direct you to the **Genome Assembly Search and Request
page.**
Steps to request an assembly:
1. Enter the **species name, common name, or GC accession number** of the assembly.
2. Click the **request button**.
3. Fill out the required information on the submission page.
```image
src=/images/tutorialImages/assemblyRequest.png
width=100%
```
Clicking the **View sequences** link directs users to the **Assembly Browser Sequences** page. This
page displays information about chromosomes, sequences, and contigs for the selected assembly.
The third column displays alias sequence names, while subsequent columns show alternate naming
schemes. These include:
- **assembly** - Names from NCBI's assembly_report.txt file.
- **genbank** - INSDC names.
- **refseq** - Names from RefSeq annotations.
---
### Assembly details on the Gateway Page
The **Gateway Page** provides various details about an assembly, including:
- UCSC Genome Browser assembly ID
- Common name
- Taxonomic name
- Sequencing/Assembly provider ID
- Assembly date
- Assembly type
- Assembly level
- Biosample
- Assembly accession
- NCBI Genome ID
- NCBI Assembly ID
- BioProject ID
The Gateway page also offers **download links** for data files related to the genome assembly.
Once an assembly is selected, users can search for specific genome locations using:
- Genome positions (e.g., chr1:1000000-2000000)
- Gene names (e.g., BRCA1)
For more details on valid position queries, visit the [Querying the Genome Browser](/goldenPath/help/query.html) page.