0a6c6ae0e873e8c95fc1d6a941a26b50d7e92f36 mspeir Wed Sep 16 11:40:45 2026 -0700 Add a blank line after the horizontal rules in the gb101 and gateway tutorials, no Redmine These two pages put a bare --- rule directly above the next heading or div. Pandoc reads a line of dashes as either a horizontal rule or a table rule depending on what follows it, so the parse can flip when the block underneath changes. It resolves to a rule today, but converting the divs on these pages to fenced divs was enough to turn 5 sections of gb101 into tables and drop every <hr>. The blank line removes the ambiguity. The built HTML is byte-identical before and after. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git docs/tutorials/gb101.md docs/tutorials/gb101.md index ca0177251af..e5b6e9f23e6 100644 --- docs/tutorials/gb101.md +++ docs/tutorials/gb101.md @@ -83,30 +83,31 @@ Several of these drop-downs are useful for most users: - Genomes - switch between the many genomes available. - Genome Browser - configure the display, search for tracks, load a Recommended Track Set, and reset the Genome Browser back to the default settings. - Tools - access to features such as [BLAT](/cgi-bin/hgBlat), [isPCR](/cgi-bin/hgPcr), and [LiftOver](/cgi-bin/hgLiftOver). The [Table Browser](/cgi-bin/hgTables) can also export track data in various file formats. - Downloads - download sequence and annotation data in bulk, along with our command-line utilities. - My Data - create stable short links ([Sessions](/cgi-bin/hgSession)) and visualize your own data via [custom tracks](/cgi-bin/hgCustom) or [track hubs](/cgi-bin/hgHubConnect). - View - save the current image as a PDF, get the DNA sequence for the window, or open the region in an external tool. - Help - access contact information, FAQs, and Browser Documentation. </div> </div> --- + ### Using the Search Box <div class="row"> <div class="col-md-6"> The search bar allows you to navigate to a region on the genome using [genome coordinates](https://genome-blog.soe.ucsc.edu/blog/2016/12/12/the-ucsc-genome-browser-coordinate-counting-systems/), [gene symbols](https://genome.ucsc.edu/FAQ/FAQgenes.html#genename), [rsIDs](https://www.ncbi.nlm.nih.gov/snp/docs/RefSNP_about/#what-is-a-reference-snp), [HGVS](http://varnomen.hgvs.org/) terms, or DNA sequence. You can even search documentation and FAQ pages using this search bar. A few example queries are: - chr1:127140001-127140001 - SOD1 - rs2569190 @@ -125,231 +126,240 @@ The [examples](https://genome.ucsc.edu/goldenPath/help/query.html) link next to the search bar contains even more search queries. </div> <div class="col-md-6"> ```image src=/images/hgTracksSearchBarExample.png width=95% ``` </div> </div> --- + ### Highlights and Zooming <div class="row"> <div class="col-md-6"> ```image src=/images/highlightZoomGif.gif width=100% ``` </div> <div class="col-md-6"> Dragging the Genome Browser image performs different tasks depending on where and how you click the image. Click-and-Drag the ruler at the top of the image will bring up a menu to zoom into or highlight the region. Click-and-Drag anywhere else on the Genome Browser image to scroll to the left or right. Alternatively, you can: - Hold **Alt+drag** or **Option+drag** to highlight - Hold **Ctrl+drag** or **Cmd+drag** to zoom </div> </div> --- + ### Configuring Data Track Display <div class="row"> <div class="col-md-6"> Clicking on the rectangle box next to a track is an easy way to go to that track's settings page quickly. [Right-clicking](/goldenPath/help/hgTracksHelp.html#RIGHT_CLICK_NAV) on the track will also bring up a menu to change the display mode, configure a track, or view a PNG image of the current window. </div> <div class="col-md-6"> ```image src=/images/rightClickAndGreyBarGif.gif width=95% ``` </div> </div> --- + ### Track Display Modes <div class="row"> <div class="col-md-6"> ```image src=/images/trackVisExamples.png width=95% ``` </div> <div class="col-md-6"> Annotation tracks can be entirely hidden or shown in four different ways that take an increasing amount of vertical space: [dense, squish, pack, and full](/goldenPath/help/hgTracksHelp.html#TRACK_CONT). *Pack display is the recommended visibility for most data types as it provides the best balance of information and space.* After changing a track's display mode, the change will not be applied until you refresh the page. You can either refresh the page manually using your web browser or click <button>refresh</button> on any of the track groups. </div> </div> --- + ### Searching for Data Tracks <div class="row"> <div class="col-md-6"> Having trouble finding a dataset for your genome assembly? The [Track Search](/cgi-bin/hgTracks?hgt_tSearch=track+search) feature allows searching for terms in track names, descriptions, groups, and ENCODE metadata. More information about <button>track search</button> can be found on the following [help page](/goldenPath/help/trackSearch.html). The Track Search feature can also be accessed by hovering over the "Genome Browser" drop-down menu. </div> <div class="col-md-6"> ```image src=/images/trackSearchSimpleExample.png width=90% ``` </div> </div> --- + ### Configuring the Genome Browser Display <div class="row"> <div class="col-md-6"> ```image src=/images/configureGif.gif width=90% ``` </div> <div class="col-md-6"> Use the <button>configure</button> button to customize graphic font, size, gridlines, and more. This can be helpful when exporting an image for publication. You can also find a link to configure the browser image by hovering over the "Genome Browser" drop-down menu. </div> </div> --- + ### Viewing the Reverse Strand <div class="row"> <div class="col-md-6"> By default, the UCSC Genome Browser displays the forward strand (5' to 3') but can be configured to display the negative strand (3' to 5'). To reverse the genome orientation, click the <button>reverse</button> button, and the Genome Browser image will flip to show either the negative or positive strand. </div> <div class="col-md-6"> ```image src=/images/reverseStrand.png width=90% ``` </div> </div> --- + ### Recommended Track Sets <div class="row"> <div class="col-md-6"> ```image src=/images/recommendedTrackSets.png width=95% ``` </div> <div class="col-md-6"> Recommended Track Sets are ready-made groups of tracks designed for specific purposes. Each set turns on a specific set of tracks and pre-configures those to aid in answering a particular question, such as interpreting clinical variants. Choosing a set switches on the relevant tracks without moving you away from your current location. Open the list from the **Genome Browser** menu in the top blue bar. </div> </div> --- + ### Sharing a Link to Your View <div class="row"> <div class="col-md-6"> The **Share a link** button in the top-right corner turns your current view into a short, permanent link that captures the assembly, position, and all of your track settings. The link never expires, so it works well in emails, figure legends, and published papers. Log in first if you would like to give your links a name or update them later. To save and reload a full setup of your own, use the **Sessions** tool under the My Data menu. </div> <div class="col-md-6"> ```image src=/images/shareLinkExample.png width=100% ``` </div> </div> --- + ### Getting Help Using the Genome Browser <div class="row"> <div class="col-md-6"> ```image src=/images/gettingHelp.png width=40% ``` </div> <div class="col-md-6"> The [training page](/training/) has other guides and training videos. You can also search the [mailing list archive](https://groups.google.com/a/soe.ucsc.edu/g/genome)