bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index fc89a00a535..404e03c2c20 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -148,31 +148,31 @@ access to Genome Browsers on several different genome assemblies. To get started, click the Browser link on the blue sidebar. This will take you to a Gateway page where you can select which genome to display. Note that there are also official <a href="genomeEuro.html">mirror sites</a> in Europe and Asia for users who are geographically closer to those continents than to the western United States.</p> <h6>Opening the Genome Browser at a specific position</h6> <p> To get oriented in using the Genome Browser, try viewing a gene or region of the genome with which you are already familiar, or use the default position. To open the Genome Browser window:</p> <ol> <li> Select the clade, genome and assembly that you wish to display from the corresponding pull-down menus. Assemblies are typically named by the first three characters of an organism's genus and species names. For older assemblies that are no longer available from the menu, the data may still - be available on our <a href="http://hgdownload.soe.ucsc.edu/downloads.html" + be available on our <a href="http://hgdownload.gi.ucsc.edu/downloads.html" target="_blank">Downloads</a> page.</li> <li> Specify the genome location you'd like the Genome Browser to open to. To select a location, enter a valid position query in the <em>search term</em> text box at the top of the Gateway page or accept the default position already displayed. The search supports several different types of <a href="query.html">queries</a>: gene symbols, mRNA or EST accession numbers, chromosome bands, descriptive terms likely to occur in GenBank text, or specific chromosomal ranges.</li> <li> Click the <em>submit</em> button to open up the Genome Browser window to the requested location. In cases where a specific term (accession, gene name, etc.) was queried, the item will be highlighted in the display.</li> </ol> <p> Occasionally the Gateway page returns a list of several matches in response to a search, rather than immediately displaying the Genome Browser window. When this occurs, click on the item in which @@ -994,31 +994,31 @@ <li> To display a details page with additional information about a specific line item within a track in full display mode, click on the item or its label.</li> <li> A track does not appear in the browser if its display mode is set to <em>hide</em>. To restrict the browser's display to only those tracks in which you're interested, set the display mode of the unwanted tracks to <em>hide</em>.</li> <li> A track set to <em>full</em> display mode will default to a more tightly packed display mode if the total number of lines in the track exceeds 250.</li> <li> To quickly toggle between <em>full</em> and <em>dense</em> or <em>pack</em> display modes, click on the track's center label.</li> <li> Only the most recent assemblies are fully active. The data for older assemblies may be available - on our <a href="http://hgdownload.soe.ucsc.edu/downloads.html" target="_blank">Downloads</a> + on our <a href="http://hgdownload.gi.ucsc.edu/downloads.html" target="_blank">Downloads</a> page.</li> <li> Not all tracks appear in all assemblies. Only a basic set of tracks appears initially in a new assembly.</li> <li> Track data can be viewed as text tables using the <a href="#TableBrowser">Table Browser</a>.</li> <li> <a href="../credits.html" target="_blank">Credit</a> goes to many individuals and institutions for generously contributing the tracks. For specific information about the contributors of a given track, look at the Credits section on a track's description page.</li> </ul> <a name="TableBrowser"></a> <h2>Getting started on the Table Browser</h2> <p> @@ -1366,87 +1366,87 @@ </dd> <dd><i>[default: off]</i></dd> </dl> </li> </ul> <h3>Command-line coordinate lifting</h3> <p> The command-line version of liftOver offers the increased flexibility and performance gained by running the tool on your local server. See an example of <a href="../../FAQ/FAQdownloads.html#liftOver">running the liftOver tool</a> on the command line. This utility requires access to a Linux platform. The executable file may be downloaded <a href="https://genome-store.ucsc.edu">here</a>. Command-line liftOver requires a UCSC-generated <em>over.chain</em> file as input. Pre-generated files for a given assembly can be accessed from the assembly's "LiftOver files" link on -the <a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> page. If the desired +the <a href="http://hgdownload.gi.ucsc.edu/downloads.html">Downloads</a> page. If the desired conversion file is not listed, send a request to the <a href="../../contacts.html">genome mailing list</a> and we may be able to generate one for you. For use of the command-line version of LiftOver, we require all for-profit businesses or commercial companies to <a href="https://genome-store.ucsc.edu/">purchase a license</a> to support our small team.</p> <a name="Download"></a> <h2>Downloading genome data</h2> <p> Most of the underlying tables containing the genomic sequence and annotation data displayed in the Genome Browser can be downloaded. All of the tables are freely usable for any purpose except as indicated in the README.txt file in the download directories. This data was contributed by many researchers, as listed on the Genome Browser <a href="../credits.html" target="_blank">Credits</a> page. Please acknowledge the contributor(s) of the data you use. <h3>Downloading the data</h3> <p> Genome data can be downloaded in different ways using our North American and European download servers, hgdownload, hgdownload2, and hgdownload-euro.</p> <dl> <dt>Via rsync:</dt> <dd> The UCSC Genome Browser hgdownload server contains download directories for all genome versions currently accessible in the Genome Browser. Either of the following rsync commands can quickly and efficiently download large files to your current directory (./).</dd> - <pre><code>rsync -a -P rsync://hgdownload.soe.ucsc.edu/path/file ./</code></pre> + <pre><code>rsync -a -P rsync://hgdownload.gi.ucsc.edu/path/file ./</code></pre> <pre><code>rsync -a -P rsync://hgdownload2.soe.ucsc.edu/path/file ./</code></pre> <pre><code>rsync -a -P rsync://hgdownload-euro.soe.ucsc.edu/path/file ./</code></pre> <dd> To download an entire directory (note the trailing slash), you would use an expression such as:</dd> - <pre><code>rsync -a -P rsync://hgdownload.soe.ucsc.edu/directory/ ./</code></pre> + <pre><code>rsync -a -P rsync://hgdownload.gi.ucsc.edu/directory/ ./</code></pre> <pre><code>rsync -a -P rsync://hgdownload2.soe.ucsc.edu/directory/ ./</code></pre> <pre><code>rsync -a -P rsync://hgdownload-euro.soe.ucsc.edu/directory/ ./</code></pre> <dd> For more information please click <a href="../help/ftp.html" target="_blank">here</a>.</dd> <dt>Via ftp:</dt> <dd> The UCSC Genome Browser FTP server contains download directories for all genome versions currently accessible in the Genome Browser. The FTP URLs - <code>ftp://hgdownload.soe.ucsc.edu/goldenPath/</code>, + <code>ftp://hgdownload.gi.ucsc.edu/goldenPath/</code>, <code>ftp://hgdownload2.soe.ucsc.edu/goldenPath/</code>, or <code>ftp://hgdownload-euro.soe.ucsc.edu/goldenPath/</code> will take you to a directory that contains the genome download directories. This download method is not recommended if you plan to download a large file or multiple files from a single directory compared to rsync (see above). You can, however, use the <code>mget</code> command to download multiple files: <code>mget <em>filename1 filename2</em></code>, or <code>mget -a</code> (to download all the files in the directory).</dd> <dt>Via the Downloads link:</dt> <dd> Click the - <a href="http://hgdownload.soe.ucsc.edu/downloads.html" target="_blank">Downloads</a> link on + <a href="http://hgdownload.gi.ucsc.edu/downloads.html" target="_blank">Downloads</a> link on the left side bar on the UCSC Genome Browser home page to display a list of all database directories available for download. If the data you wish to download pre-dates the assembly versions listed, look for the data on our - <a href="http://hgdownload.soe.ucsc.edu/downloads.html" target="_blank">Downloads</a> page.</dd> + <a href="http://hgdownload.gi.ucsc.edu/downloads.html" target="_blank">Downloads</a> page.</dd> <dt>Via the REST API:</dt> <dd> The <a href='./api.html' target=_blank>REST API</a> can be used to query both annotation and sequence data from any UCSC genome assembly or hub.</dd> </dl> <h3>Types of data available</h3> <p> There may be several download directories associated with each version of a genome assembly: the full data set <em>(bigZips)</em>, the full data set by chromosome <em>(chromosome)</em>, the annotation database tables <em>(database)</em>, and one or more sets of comparative cross-species alignments.</p> <p> <em>BigZips</em> contains the entire draft of the genome in chromosome and/or contig form. Depending on the genome, this directory may contain some or all of the following files:</p> @@ -1545,66 +1545,66 @@ <p> Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser alongside native annotation tracks. Hubs are a useful tool for visualizing a large number of genome-wide data sets. The <a href="../../cgi-bin/hgHubConnect" target="_blank">Track Hub</a> utility allows efficient access to data sets from around the world through the familiar Genome Browser interface. Browser users can display tracks from any public track hub that has been registered with UCSC. We offer <a href="publicHubGuidelines.html" target="_blank"> guidelines</a> for those who want to make a hub a public track hub. Additionally, users can import data from unlisted hubs or can set up, display, and share their own track hubs.</p> <p> For information on using the Track Hub features, refer to the <a href="hgTrackHubHelp.html">Genome Browser Track Hub User Guide</a>. For specific information on configuring your trackDb.txt file, refer to the <a href="trackDb/trackDbHub.html">Track Database Definition Document</a>. See also the <a href="hubQuickStart.html" target="_blank">Basic Hub Quick Start Guide</a>, <a href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Track Hubs into -Groupings</a>, <a href="https://genome-blog.soe.ucsc.edu/blog/2022/06/28/track-hub-settings/" +Groupings</a>, <a href="https://genome-blog.gi.ucsc.edu/blog/2022/06/28/track-hub-settings/" target="_blank">Track hub settings blog post</a>, <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs</a>, <a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable Track Hubs</a>, and <a href="/FAQ/FAQlink#hubUrl" target="_blank">Loading Track Hubs and Assembly Hubs with the URL</a>.</p> <a name="GenArkTrackHubs"></a> <h2>Track Hubs for <em>GenArk</em> assembly hub</h2> <p> To construct a track hub that will display on a -<a href='https://hgdownload.soe.ucsc.edu/hubs/' +<a href='https://hgdownload.gi.ucsc.edu/hubs/' target=_blank>GenArk Assembly</a> hub, specify the <em>GenArk</em> assembly name in the <b>genome</b> statement in your <b>hub.txt</b> file as <a href='#UseOneFile'>described below</a>. For example, a reference such as: </p> <pre> genome GCA_021951015.1 </pre> <p> will direct your track hub to display on the human <b>Feb. 2022 - GCA_021951015.1 - HG002.mat.cur.20211005</b> genome assembly. </p> <p> To share your track hub with your audience of interest, when you publish the URL to your track hub, that <b>genome</b> reference in your track <b>hub.txt</b> file will cause that associated assembly hub to display in the genome browser with your track hub annotations on that genome browser. There is no need to otherwise reference the assembly hub, it will automatically attach itself. </p> <p> A complete list of all available <em>GenArk</em> assemblies available can be seen in the text file -<a href='https://hgdownload.soe.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt' +<a href='https://hgdownload.gi.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt' target=_blank>UCSC_GI.assemblyHubList.txt</a>. </p> <a name="UseOneFile"></a> <h2>Track Hubs in a single file</h2> <p> Historically, a hub needed a set of text files to specify properties for a track hub and each of the data tracks within the hub. The track hub settings were stored in a three file structure: hub.txt, genomes.txt, and trackDb.txt</p> <pre> myHub/ - directory containing track hub files * hub.txt - a short description of hub properties * genomes.txt - list of genome assemblies included in the hub data * hg19/ - directory of data for the hg19 (GRCh37) human assembly ** trackDb.txt - display properties for tracks in this directory