6d3847d1a7c65126cb2b38f631c8b8db737efdf0 lrnassar Wed Jun 25 17:30:56 2025 -0700 Making small tweaks to the new trainings, like reducing the image width to 65% so it better fits on the screen due to the resolution, and staging various updates on our pages including the news archive announcing the release of our new tutorials page, refs #35956 diff --git docs/tableBrowserTutorial.md docs/tableBrowserTutorial.md index 9700b190e16..4a60ed81cbc 100644 --- docs/tableBrowserTutorial.md +++ docs/tableBrowserTutorial.md @@ -1,203 +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 <div class="row" style="padding-top: 15px"> <div class="col-md-4"> <div class="panel panel-default" style="padding-bottom: 10px"> <h3 class="panel-title" style="width: 100%;">Table Browser Overview</h3> A screenshot highlighting the layout and key elements of the Table Browser interface. <p style="text-align: end"> <button>[View](#table-browser-overview)</button> </p> </div> </div> <div class="col-md-4"> <div class="panel panel-default" style="padding-bottom: 10px"> <h3 class="panel-title" style="width: -webkit-fill-available;">Guided Walkthrough</h3> Step-by-step guidance for using the Table Browser to extract data for your analysis. <p style="text-align: end"> <button>[View](#guided-walkthrough)</button> </p> </div> </div> <div class="col-md-4"> <div class="panel panel-default" style="padding-bottom: 10px"> <h3 class="panel-title" style="width: -webkit-fill-available;">Interactive Tutorial</h3> An in-browser walkthrough that introduces the Table Browser interface and workflow. <p style="text-align: end"> <button>[View](../cgi-bin/hgTables?db=hg38&startTutorial=true)</button> </p> </div> </div> </div> ## Table Browser Overview ``` image src=../images/tableBrowserAnnotated.png -width=80% +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) </div> <div class="col-md-6"> ```image src=../images/assemblySelection.gif width=80% ``` </div> </div> --- <div class="row"> <div class="col-md-6"> ``` image src=../images/trackSelection.gif width=80% ``` </div> <div class="col-md-6"> ### 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. </div> </div> --- <div class="row"> <div class="col-md-6"> ### 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 <button>Data format description</button> to explore: - Table layout - Related tables - Joinable fields Use "All Tables" to list all tables for the assembly. </div> <div class="col-md-6"> ``` image src=../images/tableSelection.gif width=80% ``` </div> </div> --- <div class="row"> <div class="col-md-6"> ``` image src=../images/defineRegions.gif width=80% ``` </div> <div class="col-md-6"> ### 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 <button>Lookup</button> - Using <button>Define regions</button> to upload/paste multiple coordinates </div> </div> --- <div class="row"> <div class="col-md-6"> ### 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 </div> <div class="col-md-6"> ``` image src=../images/tutorialImages/tableBrowserOutputDropDown.png width=80% ``` </div> </div> --- <div class="row"> <div class="col-md-6"> ``` image src=../images/downloadData.gif width=80% ``` </div> <div class="col-md-6"> ### Step 6: Submit Your Query Click <button>Get output</button> to execute your query and view/download results. You can download results by entering a filename in the **output filename** field before clicking <button>Get output</button>. You can also click <button>Summary/statistics</button> to preview: - Record count - Base coverage - Item size ranges - Time to compute </div> </div> ## Additional Help - [Table Browser User Guide](https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html) - [Contact UCSC](https://genome.ucsc.edu/contacts.html)