src/hg/htdocs/allTipsRaw.html 61241bfbbff01f7888533518b5394984ee64536e

61241bfbbff01f7888533518b5394984ee64536e
lrnassar
  Tue Nov 18 12:16:57 2025 -0800
Adding new tip of the day feature. Only for .ucsc domains, it will display a new tip every weekday on the home page. The script generateTipOfDay.py runs weekdays and overwrites the tipOfDay page using the raw page, saving the used tips in a hash file on the running user (e.g. hive qateam), then recycling the list picking a random tip again once the full list has been run through. This is page and allTips page are autoPushed daily. Refs #19784

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+You can use the <a href="/cgi-bin/hgVai" target="_blank">Variant Annotation Integrator</a> to <b>predict functional effects of variants</b> on transcripts, and add annotations and information to the variants, such as <b>conservation score</b> and its <b>HGVS nomenclature</b>. It supports <b>VCF</b> upload and other formats.
+The Browser tracks display offers <b>keyboard shortcuts</b> for most common actions, including <b>zooming</b>, <b>highlighting</b>, and <b>viewing DNA</b>. Press the <b>question mark (?)</b> key from the tracks display to see all shortcuts.
+You can right-click most items to <b>zoom in</b> on them, or <b><span style="background-color: #ffff00;">highlight</span></b> them in the image. For gene tracks, you can also <b>zoom to specific exons</b> or </b>codons</b>. </p><p style="margin: 0;"><img src="/images/rightClickZoom.png" alt="Right click zoom?" style="height: 100px; width: auto; flex-shrink: 0; margin: 0;">
+You can configure the tracks display <b>font size</b>, <b>tooltip text size</b>, <b>label area width</b>, and more by clicking the <button>Configure button</button> below the image, using the keyboard shortcut (type <b>"c" then "f"</b>), or via the menu (<b>Genome Browser</b> then <b>Configure</b>).</p><p style="margin: 0;"><img src="/images/configureOptions.png" alt="Configure options" style="height: 80px; width: auto; flex-shrink: 0; margin: 0;">
+You can <b><span style="color: #00C000;">c</span><span style="color: #CC0000;">o</span><span style="color: #FFB300;">l</span><span style="color: #00C000;">o</span><span style="color: #CC0000;">r</span> and download <span style="color: #0000CC;">D</span><span style="color: #00C000;">N</span><span style="color: #CC0000;">A</span> sequence</b> based on any data tracks. While on the track display, type "v d" (<b>View - DNA</b>), then select "<b>extended case/color options</b>" and adjust whether you want annotated bases colored, underlined, or bold, and click "<b>submit</b>".
+From the <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=ruler" target="_blank">Base Position</a> track description page you can enter <b>motifs to highlight</b>, edit the <b>amino acid reading frames display</b>, and even <b>add a title</b> to the Browser image.</p><p style="margin: 0;"><img src="/images/editTitle.png" alt="Edit image title" style="height: 75px; width: auto; flex-shrink: 0; margin: 0;">
+We offer a <a href="/goldenPath/help/api.html" target="_blank">REST API</a> available under the menu (<b>Downloads</b> then <b>REST API</b>) that can return almost all data available in the Browser in <b>JSON format</b>. It also has additional endpoints, such as <b>/list/schema</b>, that can retrieve the internal organization of track data stanzas (<b>trackDb</b>), which is otherwise unavailable.
+We offer a <b>scalable</b> (vector-based) graphic of your current tracks display, suitable for use in <b>publications</b>, via the menu (<b>View</b> then <b>PDF</b>). This PDF can then be used with your editor of choice (e.g. Adobe illustrator) to edit and export the image as <b>PNG</b>, <b>TIFF</b>, <b>SVG</b>, or <b>PDF</b> with the dpi (dots per inch value) of your choice.
+You can download the <b>PNG</b> image of your current display via <b>right click</b> -> <b>View image</b>, or by changing <b>hgTracks</b> in the URL bar to <b>hgRenderTracks</b>. The hgRenderTracks approach provides <b>programmatic access</b> to the PNG image. For publications, use the menu option (<b>View</b> then <b>PDF</b>) for a scalable image.
+We offer <b>Recommended Track Sets</b> for <b>hg19</b> and <b>hg38</b> that display a pre-set browser configuration based on specific areas of interest. These include <b>SNV</b> interpretation, <b>CNV</b> interpretation, and <b>non-coding SNV</b> interpretation.</p><p style="margin: 0;"><img src="/images/recommendedTrackSetMenu.png" alt="RTS menu" style="height: 75px; width: auto; flex-shrink: 0; margin: 0;">
+The <a href="/cgi-bin/hgCollection" target="_blank">Track Collection Builder</a> (<b>My Data</b> > <b>Track Collection Builder</b>) allows multiple signal tracks to be copied and grouped together into one composite. Signal tracks in a composite container can then be <b>overlaid</b>, <b>auto-scaled</b>, <b>sorted by similarity</b>, and more.
+The best way to find what data is available for an assembly is <b>Track Search</b>, found by keyboard shortcut (<b>t</b> then <b>s</b>), in the menu bar (<b>Genome Browser</b> > <b>Track Search</b>) or the <button>Track search</button> button underneath the tracks image. You can also search <b>Public Hub data</b> by using the <b>Advanced</b> tab.
+We offer <b>10Gb of free storage space</b> to every user. First, <a href="/cgi-bin/hgSession" target="_blank">log in</a> or <a href="/cgi-bin/hgSession" target="_blank">create an account</a>, then go to <a href="/cgi-bin/hgHubConnect#hubUpload" target="_blank">Hub Upload</a> under <b>My Data</b> > <b>Track Hubs</b>. You can also upload <b>bigBed</b> and <b>bigWig</b> files for immediate visualization.
+You can <b>download all visible data</b> in the current browser region from the tracks display. This allows for improved reproducibility, writing variant reports, or publications. <b>Download track data in view</b> can be found in the <b>Download</b> menu.</p><p style="margin: 0;"><img src="/images/downloadCurrentRegion.png" alt="Download track data in view" style="height: 115px; width: auto; flex-shrink: 0; margin: 0;">
+We support <a href="/goldenPath/help/query.html" target="_blank">various kinds of searching</a> from the tracks display address bar. You can use <b>HGVS terms</b> (NM_198056.2:c.1A>C), <b>gnomAD style variants</b> (1-55051215-G-GA), <b>BLAT sequences</b> directly from the search box, <b>documentation</b>, and more.
+We have a page that provides information about <b><a href="/accessibility.html" target="_blank">accessibility options</a></b> in the UCSC Genome Browser, including internal configuration settings and third-party tools.
+The best way to find an assembly is the <b>search box</b> on our <a href="/cgi-bin/hgGateway" target="_blank">Gateway page</a>. If your assembly of interest is not available, you can <a href="/assemblySearch.html" target="_blank">request nearly any Genbank assembly</a> as long as it has a <b>GCA</b> or <b>GCF</b> accession.
+The best way to share the URL of a Genome Browser display is with a <a href="/cgi-bin/hgSession" target="_blank">Session link</a>. Displays from copying and pasting the URL from the address bar can <b>change over time</b>, but session links remain <b>constant indefinitely</b>, making them suitable for publications as well. You can <b>even customize the backend</b>: <a href="https://genome.ucsc.edu/s/view/HappyNewYear" target="_blank">https://genome.ucsc.edu/s/view/HappyNewYear</a>
+You can slice the Browser display into different regions, <b>stitched together into a single display</b>, using <a href="/goldenPath/help/multiRegionHelp.html" target="_blank">Multi-region</a> mode. A common use of this mode is to display only the exons of a gene, which is useful when analyzing exon sequencing data. Enable this mode with the <button>Multi-region</button> button next to the tracks display search bar.</p><p style="margin: 0;"><img src="/images/multiRegionButtonTip.png" alt="Multi region button" style="height: 60px; width: auto; flex-shrink: 0; margin: 0;">
+Our <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=oligoMatch" target="_blank">Short Match</a> tool allows you to search for any <b>short (2-30 base) sequence</b>. All matches of the motif within the displayed position range are then shown. You can find it by clicking into the <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=oligoMatch" target="_blank">Short Match</a> track in the <b>Mapping and Sequencing</b> track group, or via the menu bar from the tracks display (<b>Genome Browser</b> > <b>Short Exact DNA Match</b>).
+Be sure to check our home page often! We regularly update our <a href="/newsarch.html" target="_blank">news</a> with the latest releases, our <b>Meetings and Workshops</b> (come say hello!), and the <b>Sharing data</b> section which displays images and descriptions from our <a href="/cgi-bin/hgPublicSessions" target="_blank">Public Sessions</a> created by <b>users like you</b>. Also, new tips like this one <b>daily</b>!
+Want to use the Browser as a <b>teaching tool</b>? We offer <a href="/training/education/index.html" target="_blank">teaching modules</a> covering various genomic topics aimed at an <b>undergraduate</b> level. We also have various slide decks, <a href="/training/education/contacts.html" target="_blank">contact us</a> for more details!
+You can <b>convert annotations</b> between different assemblies using the <a href="/cgi-bin/hgLiftOver" target="_blank">LiftOver tool</a>. You can also use the <b>QuickLift</b> feature to immediately lift <b>all your visible annotations</b> from the tracks display using the menu (<b>View</b> > <b>In Other Genomes</b>) and selecting the <b>QuickLift tracks</b> box.
+While the <a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> allows you to extract data from <b>one source</b>, the <a href="/cgi-bin/hgIntegrator" target="_blank">Data Integrator</a> allows you to select track items that overlap by position, and <b>output all</b> (or selected) fields from up to <b>5 tracks at a time</b>.