677cd59d724e321a375348bb1ce738ee74156672 mspeir Sat Mar 28 16:57:36 2026 -0700 Fixing typo in link, refs #35259 diff --git src/hg/htdocs/allTipsRaw.html src/hg/htdocs/allTipsRaw.html index 94479496910..2b509a21fc0 100644 --- src/hg/htdocs/allTipsRaw.html +++ src/hg/htdocs/allTipsRaw.html @@ -10,16 +10,16 @@ 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="/goldenPath/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="/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>. -Have you ever wondered what we mean by "track" or what the difference is between "haplotype" and "fix" sequences? Take a look at the <a href="/docs/genomeBrowserGlosasry.html" target="_blank">Genome Browser Glossary</a> page for an explanation of these terms and many more. +Have you ever wondered what we mean by "track" or what the difference is between "haplotype" and "fix" sequences? Take a look at the <a href="/docs/genomeBrowserGlossary.html" target="_blank">Genome Browser Glossary</a> page for an explanation of these terms and many more.