9c4464a8b6f85855c9e758f04f0b811403efb64f
lrnassar
Thu Sep 19 16:00:34 2024 -0700
Adding a new --filter to the pandoc run linking to a file with special cases we want handled by the conversion. This first case takes an image code block and converts it to an html image tag with source and width specified. Refs #30335
diff --git docs/gb101.md docs/gb101.md
index c818ab4..7984535 100644
--- docs/gb101.md
+++ docs/gb101.md
@@ -1,166 +1,171 @@
% Genome Browser Tutorials
# Introduction to the UCSC Genome Browser
This page attempts to introduce you to the basics of using the UCSC Genome Browser including:
- Basic Navigation
- Basic Table Browser Query
- Basic BLAT Query
## Sections
Use the sections below to learn about the UCSC Genome Browser interface.
Genome Browser Interface
Annotated screenshot of the Genome Browser interface. Explains what all the buttons do
Guided Workthrough
Explains the basis of using/navigating the Genome Browser interface.
Also explains a very basic Table Browser query and BLAT query.
Interactive Tutorial
Steps you through the basic functionality in the Genome Browser itself.
## Annotated Screenshot
+```image
+src=../images/annot-screenshot-sarCov2.jpg
+width=30%
+```
+
| Item | Explanation |
|------|-------------|
| Menu | Find BLAH |
-(Wee need something below the table otherwise later markdown isn't properly interpreted)
+(We need something below the table otherwise later markdown isnt properly interpreted)
## Guided Workthorugh
This walkthrough will take you through the basic Genome Browser functionality.
By the end of the workthrough you should be able to do these three things:
1. Naviagte the Genome Browser Interface
2. Perform a basic Table Browser query
3. Perform a simple BLAT query
### Genome Browser Basics
In this guided walkthrough, we go from selecting our genome (hg38 in this
case), to going to our gene of interest (BLAH), to turning off and on some of
our favorite tracks, before finally BLAH.
#### Step 1: Choose your genome
Go to BLAH, select your genome from the diagram or search for in the search box at the top left of the screen.
For this walkthrough, we will select "Human" and stick with the default GRCh38/hg38 assembly.
#### Step 2: Navigate to your gene of interest
After selecting a genome, enter a gene name into the search box. In our case,
we will enter "HUNK", a gene for BLAH, into the search box.
After typing in the name, select the gene name "HUNK" from the list that
appears below the search box. You will be taken directly to that gene location.
#### Step 3: Configure the Genome Browser tracks
The horizontal lines of genomic data in the UCSC Genome Browser are known as **tracks**. they may BLAH, BLAH, and BLAH
