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/customTrackTutorial.md docs/tutorials/customTrackTutorial.md index 5ebb1da425f..cc0853af9e0 100644 --- docs/tutorials/customTrackTutorial.md +++ docs/tutorials/customTrackTutorial.md @@ -1,202 +1,220 @@ % UCSC Genome Browser Custom Track Tutorial The UCSC Genome Browser allows users to load their own annotations by adding [Custom Tracks](../cgi-bin/hgCustom). Custom tracks work well for quickly displaying data and are automatically discarded 48 hours after the last time they were accessed. This tutorial introduces the Custom Track interface and demonstrates how to: - Select a genome and assembly - Define a region of interest - Format the custom track - Load a custom track into the Genome Browser - Manage custom tracks ## 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%;">Custom Track Overview</h3> A screenshot highlighting the layout and key elements of the Custom Track interface. <p style="text-align: end"> <button>[View](#custom-track-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 Custom Track interface to upload 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 Custom Track interface and workflow. <p style="text-align: end"> <button>[View](/cgi-bin/hgCustom?db=hg19&startCustomTutorial=true&hgct_do_add=1)</button> </p> </div> </div> </div> ## Custom Track Overview <h6>Add Custom Tracks</h6> ``` image src=/images/tutorialImages/hgCustomAnnotated_pt1.png width=65% ``` <h6>Manage Custom Tracks</h6> ``` image src=/images/tutorialImages/hgCustomAnnotated_pt2.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 **Change selected genome** search box to switch assemblies. Type a species name, common + name, or assembly ID, then choose one from the list. **Current Genome** shows which assembly is + active. </div> <div class="col-md-6"> ```image src=/images/tutorialImages/gif/hgCustomStep1.gif width=90% ``` </div> </div> --- <div class="row"> <div class="col-md-6"> ```image src=/images/tutorialImages/gif/hgCustomStep2.gif width=90% ``` </div> <div class="col-md-6"> ### Step 2: Create a browser line The [browser line](/goldenPath/help/customTrack.html#BROWSER) controls where you are first taken after uploading the custom track. This step controls the aspects of the overall display window. For example, if the browser line `browser position chr22:1-20000` is used, the Genome Browser window will initially display the first 20,000 bases of chromosome 22. Browser lines are in the format: browser attribute_name attribute_value(s) </div> </div> --- +### The track line + +Along with the browser line, a **track line** sits above your data and sets what the track is +called and how it looks. It is optional for a quick look, but worth adding if you plan to keep +or share the track. Common attributes: + +- `name` — the short label shown to the left of the track +- `description` — the longer text shown in the track's title and details page +- `visibility` — how the track is drawn: `hide`, `dense`, `squish`, `pack`, or `full` +- `color` — the feature color as RGB values, for example `color=0,0,255` for blue + +A track line looks like: + + track name="My variants" description="Sample calls" visibility=pack color=0,0,255 + +For bigBed, bigWig, bigGenePred, CRAM, BAM, and VCF files you can skip the track line and +paste just the URL to the file, one per line. + +--- + <div class="row"> <div class="col-md-6"> ### Step 3: Format the Data The annotation data must be formatted into one of the [supporting formats](/FAQ/FAQformat.html). For many formats, chromosome names can either be UCSC-style names (e.g. 'chr1', 'chrX') or [aliases](/FAQ/FAQcustom.html#custom12) from other sources (e.g. '1' or 'NC\_000001.11'). While most data types can be uploaded directly to UCSC, any of the binary-indexed files must be hosted on an external server. This includes formats such as bigBed, bigWig, BAM, VCF, and other big\* files. A few hosting resources that we recommend can be found on the [Hosting](/goldenPath/help/hgTrackHubHelp.html#Hosting) help page. </div> <div class="col-md-6"> ```image src=/images/tutorialImages/gif/hgCustomStep3.gif width=90% ``` </div> </div> --- <div class="row"> <div class="col-md-6"> ```image src=/images/tutorialImages/gif/hgCustomStep4.gif width=90% ``` </div> <div class="col-md-6"> ### Step 4: Load the custom track Once the Browser and track lines are created, you can upload the custom track to the UCSC Genome Browser using the dialogue box or the <button>Choose File</button> button to upload the custom track file. When using a custom track file, you can also paste the URL to the custom track to quickly load your annotations. We recommend adding documentation to your custom annotation tracks, especially if you intend to share the annotations with other collaborators. </div> </div> --- <div class="row"> <div class="col-md-6"> ### Step 5: Manage custom tracks page Click <button>Submit</button> to upload the data to the UCSC Genome Browser. You will be taken to a new page where you can view all your uploaded custom tracks. Here, you can edit the annotation data, or remove any custom tracks. There is also a drop-down menu to view the data in other tools, such as: - Genome Browser - Table Browser - Data Integrator - Variant Annotation Integrator Clicking on the chromosome hyperlink, e.g. chr21, in the table will take you to the Genome Browser image to view the data. </div> <div class="col-md-6"> ```image src=/images/tutorialImages/gif/hgCustomStep5.gif width=90% ``` </div> </div> ## Additional Help - [Custom Track User Guide](/goldenPath/help/customTrack.html) - [Contact UCSC](/contacts.html)