3400f3754a96dc0bf52ee14a4839fb0abac26d20
gperez2
Mon May 19 09:12:32 2025 -0700
Updating location for images and the interactive tutorial url, refs #34938
diff --git docs/gatewayTutorial.md docs/gatewayTutorial.md
index c71df758523..f2286aaa21d 100644
--- docs/gatewayTutorial.md
+++ docs/gatewayTutorial.md
@@ -37,52 +37,52 @@
Interactive Tutorial
An interactive tutorial that covers the basic Browser introduction on the Gateway page.
-
+
## Gateway page screenshot
```image
-src=../images/gatewayPageAnnotated.jpg
+src=../images/tutorialImages/gatewayPageAnnotated.jpg
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.
---
@@ -99,72 +99,72 @@
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
The **Species Tree** option displays a phylogenetic tree that can be navigated using scrolling or
by clicking different parts of the tree. Hovering over a branch will reveal 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.
@@ -177,55 +177,55 @@
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.
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.
@@ -248,50 +248,50 @@
- 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.