3b69a19fd83cdcbace0acc21c321fd241f162b44 jnavarr5 Tue Jun 24 16:37:34 2025 -0700 Creating the Table Browser tutorial markdown, refs #35126 diff --git docs/tableBrowserTutorial.md docs/tableBrowserTutorial.md new file mode 100644 index 00000000000..9700b190e16 --- /dev/null +++ docs/tableBrowserTutorial.md @@ -0,0 +1,203 @@ +% UCSC Genome Browser Table Browser Tutorial + +The [UCSC Table Browser](../cgi-bin/hgTables) is a flexible tool for accessing and exporting data from genome browser tracks. This tutorial introduces the Table Browser interface and demonstrates how to: + +- Select a genome and assembly +- Choose a track and table +- Define a region of interest or use identifiers +- Customize output formats +- Download or view extracted results + +## Learning materials + +
+
+
+

Table Browser Overview

+ +A screenshot highlighting the layout and key elements of the Table Browser interface. + +

+ +

+
+
+ +
+
+

Guided Walkthrough

+ +Step-by-step guidance for using the Table Browser to extract data for your analysis. + +

+ +

+
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+ +
+
+

Interactive Tutorial

+ +An in-browser walkthrough that introduces the Table Browser interface and workflow. + +

+ +

+
+
+
+ +## Table Browser Overview + +``` image +src=../images/tableBrowserAnnotated.png +width=80% +``` + +--- + +## Guided Walkthrough + + +
+
+### 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) +
+ +
+ ```image + src=../images/assemblySelection.gif + width=80% + ``` +
+
+ +--- + + +
+
+ ``` image + src=../images/trackSelection.gif + width=80% + ``` +
+ +
+### Step 2: Select a Track + Choose the data track you want to work with. The Table Browser will pre-select your most recent track, but you can change it. + + - Tracks are grouped similarly to those on the Genome Browser main page. + - Use "All Tracks" for comprehensive options. +
+
+ +--- + + +
+
+### Step 3: Select the Table + + Each track may have one or more associated tables that store the data. Use the **Table** menu to select the relevant one. + + Click the to explore: + + - Table layout + - Related tables + - Joinable fields + + Use "All Tables" to list all tables for the assembly. + +
+ +
+ ``` image + src=../images/tableSelection.gif + width=80% + ``` +
+
+ +--- + + +
+
+ ``` image + src=../images/defineRegions.gif + width=80% + ``` +
+ +
+### Step 4: Define a Genomic Region + You can limit the output to a specific region or get data genome-wide. + Whole-genome output may be unavailable for some tracks due to the large amount of data. + + Options include: + + - Entering a position (e.g., `chr7:117199645-117356025`) + - Typing a gene name and clicking + - Using to upload/paste multiple coordinates + +
+
+ +--- + +
+
+### Step 5: Select Output Format + Use the **Output format** dropdown to choose what type of file or fields you want returned. + + Options include: + + - All fields from the table + - Selected fields only + - File formats like BED, GTF, or custom tracks +
+
+ ``` image + src=../images/tutorialImages/tableBrowserOutputDropDown.png + width=80% + ``` +
+
+ + +--- + +
+
+ ``` image + src=../images/downloadData.gif + width=80% + ``` +
+
+### Step 6: Submit Your Query + Click to execute your query and view/download results. + You can download results by entering a filename in the **output filename** field before clicking . + + You can also click to preview: + + - Record count + - Base coverage + - Item size ranges + - Time to compute + +
+
+ +## Additional Help + +- [Table Browser User Guide](https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html) +- [Contact UCSC](https://genome.ucsc.edu/contacts.html)