dd6958bf3e8dfeb13dad8906a5c471293c471152 mspeir Wed Jul 22 07:56:17 2026 -0700 Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> diff --git docs/tutorials/tableBrowserTutorial.md docs/tutorials/tableBrowserTutorial.md index 3d1d786c2c4..8cd87921fa9 100644 --- docs/tutorials/tableBrowserTutorial.md +++ docs/tutorials/tableBrowserTutorial.md @@ -1,203 +1,222 @@ % 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=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) + Use the **Genome** search box to choose your reference genome. Start typing a species name, + common name, or assembly ID and pick a match from the list that drops down. The Table Browser + reloads on that assembly, and **Assembly** shows which one you are using. </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 + - Pasting or uploading a list of identifiers, such as gene names or accessions, with + <button>Paste list</button> or <button>Upload list</button> to return only those items </div> </div> --- +### Optional: filter, subset, or combine tracks + +The **Filter** and **Intersection** tools, in the *Subset, combine, compare with another +track* section, let you narrow down or combine data before you get output. + +Click <button>Create</button> next to **Filter** to keep only the rows that match conditions +you set, for example genes on the plus strand or items above a score cutoff. A filter stays +in place until you clear it, so you can switch tracks or regions and rerun the same query. + +Click <button>Create</button> next to **Intersection** to combine the current track with a +second one. This answers questions like which SNPs fall inside RefSeq coding exons, or which +of your regions overlap a peak track. You pick the second track and whether to keep the rows +that overlap or the ones that don't. + +--- + <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 + - **All fields from selected table** returns the table as it is stored. + - **Selected fields from primary and related tables** lets you pick just the columns you + want, and pull in columns from related tables in the same query. This is the easiest way + to get something like gene names next to coordinates without downloading the whole table. + - File formats like **BED**, **GTF**, or a **custom track** you can load back into the browser. + - **Sequence** returns the DNA, or protein for some tracks, covered by your table. </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)