4d078885529f20b1eb60a0dbb7931ae76793a5ea lrnassar Tue Aug 4 09:24:38 2026 -0700 Fix stale alt text and copy problems in the tip rotation per CR feedback. refs #37976 The image alt text on the "Download Current Track Data" tip still carried the old incorrect label, "Download track data in view", so the correction in the previous commit only reached the visible text and left the wrong wording in the accessibility layer. Also replaced the internal "RTS" abbreviation in the Recommended Track Sets alt text with the full name. Other copy fixes: the Track Collection Builder tip called the result a "container" in one sentence and a "collection" in the next, so both now say collection to match the tool name; a "which" clause in the multi-region tip attached the exon view keyboard shortcut to "exon sequencing data" rather than to the view itself; and the Recommended Track Sets tip listed six of the seven sets, so exon relevance was added. diff --git src/hg/htdocs/allTipsRaw.html src/hg/htdocs/allTipsRaw.html index 2926d90991f..310ed650b88 100644 --- src/hg/htdocs/allTipsRaw.html +++ src/hg/htdocs/allTipsRaw.html @@ -1,47 +1,47 @@ 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 menu with zoom and highlight options" style="height: 100px; width: auto; flex-shrink: 0; margin: 0;"> You can configure the tracks display <b>text 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 <b>"v" then "d"</b> (<b>View</b> then <b>DNA Sequence</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>, which reports every field in a track along with its type and description, and <b>/list/tracks</b>, which returns the configuration settings that drive a track's display. 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> and <b>CNV</b> interpretation, <b>non-coding variants</b>, <b>problematic regions</b>, and expert panel sets for <b>BRCA1/BRCA2</b> and <b>Lynch syndrome</b>.</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> then <b>Track Collection Builder</b>) allows multiple signal tracks to be copied and grouped together into one <b>container</b>. Signal tracks in a collection can then be <b>overlaid</b>, <b>auto-scaled</b>, <b>sorted by similarity</b>, and more. +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> and <b>CNV</b> interpretation, <b>non-coding variants</b>, <b>exon relevance</b>, <b>problematic regions</b>, and expert panel sets for <b>BRCA1/BRCA2</b> and <b>Lynch syndrome</b>.</p><p style="margin: 0;"><img src="/images/recommendedTrackSetMenu.png" alt="Recommended Track Sets 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> then <b>Track Collection Builder</b>) allows multiple signal tracks to be copied and grouped together into one <b>collection</b>. Signal tracks in a collection 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> then <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>10 GB of free storage space</b> with every account. First, <a href="/cgi-bin/hgSession" target="_blank">log in or create an account</a>, then go to <a href="/cgi-bin/hgHubConnect#hubUpload" target="_blank">Hub Upload</a> under <b>My Data</b> then <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 Current Track Data</b> can be found in the <b>Downloads</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;"> +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 Current Track Data</b> can be found in the <b>Downloads</b> menu.</p><p style="margin: 0;"><img src="/images/downloadCurrentRegion.png" alt="Download Current Track Data in the Downloads menu" 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>stable</b>, which makes them suitable for publications as well. You can even give one a <b>short, readable name</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, useful when analyzing exon sequencing data, which has its own shortcut (<b>"e" then "v"</b>). 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;"> +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. That exon-only view has its own shortcut (<b>"e" then "v"</b>). 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 <b>Short Match</b> track in the <b>Mapping and Sequencing</b> track group, or via the menu bar from the tracks display (<b>Genome Browser</b> then <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>every weekday</b>! Want to use the Browser as a <b>teaching tool</b>? We offer <a href="/training/education/index.html" target="_blank">teaching material</a> covering various genomic topics, written for <b>students and educators</b> alike. 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> then <b>In Other Genomes (Convert)</b>) and selecting the <b>QuickLift tracks</b> box. See our <a href="/goldenPath/help/quickLift.html" target="_blank">QuickLift help page</a> for details. While the <a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> allows you to extract data from <b>one track at a time</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/genomeBrowserGlossary.html" target="_blank">Genome Browser Glossary</a> page for an explanation of these terms and many more. You can jump straight to an <b>exon</b> from the position box. Type <b>TP53 exon 5</b> or <b>NM_000546.6 exon 5</b> to land on that exon, or use the compact form <b>BRCA2:e.10+2</b> to land a set number of bases into the flanking intron, which is handy for inspecting splice sites. See our <a href="/goldenPath/help/query.html" target="_blank">searching help page</a> for every kind of query we accept.</p><p style="margin: 0;"><img src="/images/exonSearchTip.png" alt="Exon search in the position box" style="height: 52px; width: auto; flex-shrink: 0; margin: 0;"> Want the same data shown two ways at once? Click <b>Duplicate track</b> next to the display mode on most tracks' settings pages. The copy is its own track with <b>independent filters, colors, and display mode</b>, so a gene track can appear filtered and unfiltered at once.</p><p style="margin: 0;"><img src="/images/duplicateTrackTip.png" alt="Duplicate track link" style="height: 28px; width: auto; flex-shrink: 0; margin: 0;"> Lost track of what you have turned on? The <b>Visible Tracks</b> group sits at the top of the track list below the image and gathers <b>every track you currently have visible</b> into one place, so you can reconfigure or hide them without hunting through the track groups.</p><p style="margin: 0;"><img src="/images/visibleTracksTip.png" alt="Visible Tracks group" style="height: 56px; width: auto; flex-shrink: 0; margin: 0;"> Many track containers have a settings page that manages everything inside at once. You can <b>show or hide the whole container</b> while preserving each track's own settings, or use <b>Apply to all visible tracks</b> or <b>Apply to all tracks</b> to set display modes in bulk.</p><p style="margin: 0;"><img src="/images/containerApplyTip.png" alt="Apply visibility to all tracks" style="height: 24px; width: auto; flex-shrink: 0; margin: 0;"> You do not have to live with a track's default color. <b>Right-click</b> most annotation and signal tracks, choose <b>Change Track Color</b>, and pick from the palette. The new color applies to that track alone and stays with your session. Clear <b>Enable color override</b> to undo.</p><p style="margin: 0;"><img src="/images/trackColorTip.png" alt="Change Track Color dialog" style="height: 105px; width: auto; flex-shrink: 0; margin: 0;"> Zoom in far enough and the Browser translates every coding exon into <b>amino acids</b>. Hovering over a residue reports its <b>three letter and full name</b> along with the <b>c. and p. positions</b>. The <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=ruler" target="_blank">Base Position</a> settings page also has a <b>Complement the bases</b> checkbox for reading the minus strand. You can display <b>your own data</b> in the Browser in seconds with <a href="/cgi-bin/hgCustom" target="_blank">Custom Tracks</a> (<b>My Data</b> then <b>Custom Tracks</b>). Paste in a few lines of <b>BED</b>, <b>VCF</b>, <b>GFF</b>, or <b>WIG</b>, upload a file, or point us at a URL. No account is needed, though logging in lets you keep your data in a <b>saved session</b>. We offer <a href="/docs/" target="_blank"><b>interactive tutorials</b></a> that walk you through the Browser step by step, on the site itself. From the tracks display, open <b>Help</b> then <b>Interactive Tutorials</b> for a guided tour of the <b>tracks display</b>, the <b>Gateway</b>, the <b>Table Browser</b>, <b>Custom Tracks</b>, or a <b>clinical genetics</b> workflow.</p><p style="margin: 0;"><img src="/images/tutorialsTip.png" alt="Interactive Tutorials in the Help menu" style="height: 120px; width: auto; flex-shrink: 0; margin: 0;"> You can send the region you are looking at straight to <b>outside tools</b> using <b>View</b> then <b>In External Tools</b>, or by typing <b>"s" then "t"</b>. It hands your current sequence or coordinates to <b>CRISPOR</b>, <b>CHOPCHOP</b>, <b>Primer3Plus</b>, <b>Primer-BLAST</b>, <b>NEBCutter</b>, <b>RNAfold</b>, <b>Pfam</b>, <b>Ensembl</b>, and others, with no copying and pasting.</p><p style="margin: 0;"><img src="/images/externalToolsTip.png" alt="In External Tools in the View menu" style="height: 105px; width: auto; flex-shrink: 0; margin: 0;"> Our <a href="/cgi-bin/hgPcr" target="_blank">In-Silico PCR</a> tool (<b>Tools</b> then <b>In-Silico PCR</b>) takes a pair of <b>primer sequences</b> and returns the products they would amplify, along with the amplicon sequence and a link into the Browser. Set <b>Target</b> to a gene transcript set instead of the genome to handle <b>RT-PCR primers</b> that straddle intron boundaries. When you <a href="/cgi-bin/hgBlat" target="_blank">BLAT</a> a sequence and are not sure which organism it came from, check <b>Search all genomes</b> to align it against <b>all of our default assemblies</b> at once. It is a quick way to identify an unknown sequence or spot contamination. There is also an <b>I'm feeling lucky</b> button that takes you directly to the best hit. The <a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> does much more than dump out a table. You can paste a <a href="/goldenPath/help/hgTablesHelp.html#BatchQuery" target="_blank">list of gene names or IDs</a> to restrict the output to just those items, <b>intersect or subtract</b> one track against another, pull only <b>exons</b> or <b>upstream regions</b> rather than whole genes, and save a list of up to <b>1,000 regions</b> to reuse across queries. Most track description pages have a <b>Data Access</b> section that tells you exactly how to get that track in bulk, whether through the <a href="/cgi-bin/hgTables" target="_blank">Table Browser</a>, the <a href="/goldenPath/help/api.html" target="_blank">REST API</a>, or a direct file on our <a href="https://hgdownload.gi.ucsc.edu" target="_blank">downloads server</a>. The same page also documents the <b>methods</b>, <b>credits</b>, and <b>references</b> behind the data. You can jump straight to the <b>next annotation</b> in a track instead of dragging around looking for it. Turn on <a href="/goldenPath/help/hgTracksHelp.html#nextItem" target="_blank">Next/previous item navigation</a> on the <b>Configure</b> page and gray arrows appear beside the track label. The white arrows on genes running off the edge of the image are on by default and step through <b>exons</b> one at a time. The <button>Reverse</button> button below the tracks image, or the shortcut <b>"r" then "v"</b>, <b>reverse complements the entire display</b> and not just the DNA sequence. Every annotation flips to the minus strand, which makes a gene transcribed right to left far easier to read.</p><p style="margin: 0;"><img src="/images/reverseButtonTip.png" alt="Reverse button" style="height: 23px; width: auto; flex-shrink: 0; margin: 0;"> Beyond our <b>230 or so</b> natively hosted assemblies, our <a href="https://hgdownload.gi.ucsc.edu/hubs/" target="_blank">GenArk</a> collection offers more than <b>50,000 NCBI assemblies</b>, each already built with <b>gene annotation</b> and, for most eukaryotes, <b>repeat annotation</b> and <b>alignments</b>. We also curate <b>more than 100 public track hubs</b> that you can attach with one click from <b>My Data</b> then <b>Track Hubs</b>. Clicking a gene gives you far more than coordinates. The gene details page offers <b>mRNA and protein sequence</b>, <b>genomic sequence</b> with configurable flanking bases, <b>RNA-Seq expression</b>, <b>protein domains and 3-D structures</b>, <b>orthologs in other species</b>, <b>GO annotations</b>, <b>pathways</b>, disease links from <b>MalaCards</b> and <b>GeneReviews</b>, and a graph of published <b>gene interactions</b>. Has your display gotten cluttered? The <button>Hide all</button> button below the tracks image, or the shortcut <b>"h" then "a"</b>, clears every track at once. For a completely fresh start, <b>Genome Browser</b> then <b>Reset All User Settings</b> restores the original defaults. Note that a reset also removes your custom tracks and attached hubs, so save a session first if you want to keep them. Have a question about the Browser or the data in it? Our <a href="/contacts.html" target="_blank">public mailing list</a> is answered by the people who build and curate the Browser, and the archive is <b>publicly searchable</b>, so you can often find your answer before asking. There is also a <b>private list</b> for questions involving confidential data, and a low volume <b>announcements list</b> for new releases. Our <a href="/goldenPath/help/posters.html" target="_blank">Poster Gallery</a> collects more than <b>30 conference posters</b> we have presented since 2015, each a one page tour of a set of features. Topics include <b>variant interpretation</b>, <b>track hub storage</b>, <b>quickLift</b>, <b>pangenome data</b>, and <b>transposable elements</b>, and every one is free to download.</p><p style="margin: 0;"><img src="/images/posterGalleryTip.png" alt="Poster gallery" style="height: 110px; width: auto; flex-shrink: 0; margin: 0;"> Not sure what sequences an assembly actually contains? <b>View</b> then <b>Chromosomes</b>, or the shortcut <b>"v" then "s"</b>, lists every chromosome and scaffold with its size, and offers the assembly's <b>chrom.sizes</b> and <b>alias name</b> files to download. This is especially handy on newer or less familiar assemblies, where the sequence names may not be what you expect.</p><p style="margin: 0;"><img src="/images/viewChromosomesTip.png" alt="Chromosome list" style="height: 74px; width: auto; flex-shrink: 0; margin: 0;"> Assemblies often carry several names for the same sequence. Hover the <b>information icon</b> beside the position to see the alternatives, such as <b>17</b>, <b>CM000679.2</b>, and <b>NC_000017.11</b> for human chr17. Any of these names will work in the <b>position box</b> and in your own <b>custom tracks</b>, <b>hubs</b>, and <b>bigBed</b> or <b>bigWig</b> files, so there is no need to convert first.