5709a7858d5c197721be66d5218a79124abadb70 lrnassar Tue Mar 17 08:46:31 2026 -0700 Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254 diff --git src/hg/htdocs/goldenPath/help/hgConvert.html src/hg/htdocs/goldenPath/help/hgConvert.html index 615e6406283..58d24052dcf 100755 --- src/hg/htdocs/goldenPath/help/hgConvert.html +++ src/hg/htdocs/goldenPath/help/hgConvert.html @@ -1,147 +1,147 @@ <!-- This file is included in hgVai's "Using the Variant Annotation Integrator" section. --> <!-- HREF paths are relative to cgi-bin, not goldenPath/help. --> <a name="overview"></a> <h3>Overview</h3> <p> An alignment between two DNA sequences maps every nucleotide in one sequence to a nucleotide in another sequence. By making and using <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC208784/" target="_blank">whole-genome alignments</a>, the UCSC Genome Browser always allowed users to "lift" genome annotations to another assembly (<a href="/cgi-bin/hgLiftOver" target="_blank">liftOver</a>), in bulk, one track at a time. <font color="#008000">QuickLift</font> is a tool that uses the same algorithm, but it maps (liftOver) annotations on demand, in real-time, for all visible tracks. Only the annotations in the currently visible region are lifted, so this is usually fast enough when browsing a genome. For example, <font color="#008000">QuickLift</font> can be used to map annotations from hg38 or hg19 to any of the hundreds of new human high-quality genomes in GenArk (HPRC), with almost no additional delay. For instance, you can view GENCODE genes from hg38 on a T2T assembly like hs1, carrying over your visible tracks to the target genome assembly. </p> <p> <font color="#008000">QuickLift</font> functionality depends on the availability of alignment files (chains) that describe how sequences in one assembly correspond to another. The alignment files are currently made at UCSC, and if no alignment file is available for the assembly in which you're interested, please send a request to the <a href="/contacts.html" target="_blank" >genome mailing list</a>, and we will attempt to provide you with one. </p> <a name="gettingStarted"></a> <h3>Getting Started</h3> <p> The <b>source assembly</b> is the assembly where the annotations come from, and the <b>destination (target) assembly</b> is the assembly you are converting to. To use <font color="#008000">QuickLift</font>, follow these steps: </p> <ol> <li>Navigate to the genome assembly and position you want to convert in the <a href="/cgi-bin/hgTracks" target="_blank">Genome Browser</a>. Make sure the tracks you want to lift are visible.</li> <li>Open the Convert page by going to <b>View > In Other Genomes (Convert)</b> from the top menu bar, or navigate directly to the <a href="/cgi-bin/hgConvert" target="_blank">Convert page</a>.</li> <li>Under <b>Destination</b>, choose the target genome assembly. You can either: <ul> <li>Use the <b>Search</b> bar to find a target genome by name. As you type, an autocomplete dropdown appears with matching genomes. The search automatically filters results to show only assemblies that have a liftOver chain available from your source assembly. Genomes without an available liftOver chain are excluded from the results. You can also click the dropdown toggle button to browse recent and popular genomes.</li> <li>Use the <b>Assembly</b> dropdown to select from other assemblies of the same organism (e.g., other human assemblies when the source assembly is hg38). To convert to a different organism, use the Search bar instead.</li> </ul> </li> <li>Check the <b>QuickLift tracks</b> checkbox to carry over your visible tracks, custom tracks, and track hubs to the target assembly. Without this checkbox, only the coordinate position is converted. <ul> <li>When a single track from a container track, such as a superTrack or composite, is lifted, the entire container track is carried over to the target genome assembly.</li> </ul> <div class="text-center"> - <img src="../../images/QuickLift/quickLiftTracks.png" width='50%'> + <img alt="Browser view showing QuickLift converted tracks from a different assembly" src="../../images/QuickLift/quickLiftTracks.png" width='50%'> </div> </li> <li>Click <b>Submit</b>. The results page will show the corresponding position(s) in the target assembly with links to the Genome Browser. If <font color="#008000">QuickLift</font> was enabled, clicking a link will display your lifted tracks under a green "<font color="#008000">QuickLift</font> from ..." group in the target assembly. To remove <font color="#008000">QuickLift</font> tracks, click the <button>Disconnect</button> button.</li> </ol> <a name="visualIndicators"></a> <h3>Visual Indicators</h3> <p> <font color="#008000">QuickLift</font> tracks have a green left-side button bar in the Browser graphic (instead of the usual gray): </p> <div class="text-center"> -<img src="../../images/QuickLift/quickLiftGreenbuttons.png" width='7%'> +<img alt="Green QuickLift buttons used to convert coordinates between assemblies" src="../../images/QuickLift/quickLiftGreenbuttons.png" width='7%'> </div> <p> The Alignment Differences track displays liftOver differences using triangles and lines: </p> <ul> <li>Insertions: <font color="#407F00">green</font></li> <li>Deletions: <font color="#00007F">blue</font></li> <li>Double-sided insertions: <font color="#7F7F7F">gray</font> (Both the source and target assemblies contain unalignable sequence between two regions of aligned sequence)</li> <li>Mismatches: <font color="#FF0000">red</font></li> </ul> <p> Mousing over a triangle displays the size base-pair (bp) difference and the type of alignment difference. </p> <div class="text-center"> -<img src="../../images/QuickLift/quickLiftTrianglesMouseOver.png" width='70%'> +<img alt="QuickLift track with triangle markers indicating alignment differences on mouseover" src="../../images/QuickLift/quickLiftTrianglesMouseOver.png" width='70%'> </div> <p> Clicking a triangle provides the source and target assembly genome positions, DNA sequence alignment, including the type of alignment difference with the bases within the currently visible browser region.</p> <a name="unsupportedTypes"></a> <h3>Unsupported Track Formats</h3> <p><font color="#008000">QuickLift</font> does not support the following track formats:</p> <ul> <li>WIG — <a href="/goldenPath/help/bigWig.html" target="_blank">bigWig</a> is supported; WIG tracks can be converted to bigWig using the <a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>wigToBigWig</code></a> utility</li> <li>BAM</li> <li>CRAM</li> <li>PSL — <a href="/FAQ/FAQformat.html#format1" target="_blank">BED</a> is supported; PSL tracks can be converted to BED using the <a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>pslToBed</code></a> utility</li> <li>VCF</li> <li>HIC</li> <li>MAF</li> <li>bigChain</li> <li>Interact</li> <li>narrowPeak / broadPeak — <a href="/goldenPath/help/bigBed.html" target="_blank">bigBed</a> is supported; since narrowPeak and broadPeak are BED-based formats, they can be converted to bigBed using the <a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"><code>bedToBigBed</code></a> utility</li> <li>pgSnp</li> </ul> <a name="resources"></a> <h3>Resources & Support</h3> <ul> <li><a href="/cgi-bin/hgLiftOver" target="_blank">LiftOver</a> — convert coordinates or annotation files in bulk between assemblies</li> <li><a href="/goldenPath/help/chain.html" target="_blank">Chain format</a> — description of the alignment chain files used by <font color="#008000">QuickLift</font> and liftOver</li> <li><a href="/contacts.html" target="_blank">Contact us</a> — request a new liftOver chain or report issues via the genome mailing list</li> </ul>