bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html index 18521bfd542..b0dc6588d8c 100755 --- src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html +++ src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html @@ -1,25 +1,25 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Public Hub Guidelines" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Assembly</h1> <p> Please note, if you are working with a genome that has already been submitted to the <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/">NCBI Assembly</a> system, it may already be available in the <a href="https://genome.ucsc.edu">UCSC Genome Browser</a>.</p> -<p>Please examine the <a href="https://hgdownload.soe.ucsc.edu/hubs/">GenArk Assembly Hub</a> collection to see if your genome of interest is already available. In the case it cannot be found there, you can use the <a href="https://genome.ucsc.edu/assemblyRequest">UCSC Assembly Request</a> page to request a genome assembly be added to the <a href="https://genome.ucsc.edu/">UCSC Genome Browser</a>. +<p>Please examine the <a href="https://hgdownload.gi.ucsc.edu/hubs/">GenArk Assembly Hub</a> collection to see if your genome of interest is already available. In the case it cannot be found there, you can use the <a href="https://genome.ucsc.edu/assemblyRequest">UCSC Assembly Request</a> page to request a genome assembly be added to the <a href="https://genome.ucsc.edu/">UCSC Genome Browser</a>. </p> <h2>Contents</h2> <h6><a href="#overview">Overview</a></h6> <h6><a href="#webServer">Web Server</a></h6> <h6><a href="#linkingHub">Linking to Your Assembly Hub</a></h6> <ul style="margin-left: 20px;"> <li><a href="#hubTxt">hub.txt</a></li> <li><a href="#genomesTxt">genomes.txt</a></li> <li><a href="#twoBitFile">2bit File</a></li> <li><a href="#groupsTxt">groups.txt</a></li> </ul> <h6><a href="#buildingTracks">Building Tracks</a></h6> <ul style="margin-left: 20px;"> <li><a href="#cytobandTrack">Cyotoband Track</a></li> @@ -161,31 +161,31 @@ <li>The <strong>trackDb</strong> refers to a file which defines the tracks to place on this genome assembly. The format of this file is described in the Track Hub help reference documentation.</li> <li>The <strong>groups</strong> refers to a file which defines the track groups on this genome browser. Track groups are the sections of related tracks grouped together under the primary genome browser graphics display image.</li> <li>The <strong>description</strong> will be displayed for user information on the gateway page and most title pages of this genome assembly browser. It is the name displayed in the assembly pull-down menu on the browser gateway page.</li> <li>The <strong>twoBitPath</strong> refers to the .2bit file containing the sequence for this assembly. Typically this file is constructed from the original fasta files for the sequence using the kent program faToTwoBit. This line can also point to a URL, for example, if you are duplicating an existing Assembly Hub, you can use the original hub's 2bit file's URL location here.</li> <li>The <strong>organism</strong> string is displayed along with the description on most title pages in the genome browser. Adjust your names in organism and description until they are appropriate. This example is very close to what the genome browser normally displays. This organism name is the name that appears in the genome pull-down menu on the browser gateway page.</li> <li>The <strong>defaultPos</strong> specifies the default position the genome browser will open when a user first views this assembly. This is usually selected to highlight a popular gene or region of interest in the genome assembly.</li> <li>The <strong>orderKey</strong> is used with other genome definitions at this hub to order the pull-down menu ordering the genome pull-down menu.</li> <li>The <strong>htmlPath</strong> refers to an html file that is used on the gateway page to display information about the assembly.</li> <li>The <strong>transBlat</strong>, <strong>blat</strong>, and <strong>isPcr</strong> entries refer to different configurations of the gfServer that enhance search capabilities for amino acids, BLAT algorithms, and PCR respectively.<a href="https://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Preface"> More here.</a></li> </ul> <p>Note that it is strongly encouraged to give each of your genomes stanza's a line for defaultPos, scientificName, organism, description (along with other above settings) so that when your hub is attached it will load a specified default location and have text to be more easily searched from the Gateway page.</p> <a id="twoBitFile"></a> <h2>2bit File</h2> <p> - The <em>.2bit</em> file is constructed from the fasta sequence for the assembly. The <em>kent</em> source program <strong>faToTwoBit</strong> is used to construct this file. Download the program from the <a href="https://hgdownload.soe.ucsc.edu/admin/exe/">downloads</a> section of the Browser. For example: + The <em>.2bit</em> file is constructed from the fasta sequence for the assembly. The <em>kent</em> source program <strong>faToTwoBit</strong> is used to construct this file. Download the program from the <a href="https://hgdownload.gi.ucsc.edu/admin/exe/">downloads</a> section of the Browser. For example: </p> <pre> faToTwoBit ricCom1.fa ricCom1.2bit </pre> <p> Use the <strong>twoBitInfo</strong> to verify the sequences in this assembly and create a <strong>chrom.sizes</strong> file which is not used in the hub, but is useful in later processing to construct the <strong>big*</strong> files: </p> <pre> twoBitInfo ricCom1.2bit stdout | sort -k2rn > ricCom1.chrom.sizes </pre> <p> The <em>.2bit</em> commands can function with the <em>.2bit</em> file at a URL: </p> <pre> twoBitInfo -udcDir=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/ricCom1/ricCom1.2bit stdout | sort -k2nr > ricCom1.chrom.sizes