5551b0fccd8b90a7bf3f19ff7273ac5329691bb4 lrnassar Mon Mar 11 14:22:15 2024 -0700 Clarifying that only hic versions 6-8 are supported, not 9. Refs #33054 diff --git src/hg/htdocs/goldenPath/help/hic.html src/hg/htdocs/goldenPath/help/hic.html index 5c611beb..797c724 100755 --- src/hg/htdocs/goldenPath/help/hic.html +++ src/hg/htdocs/goldenPath/help/hic.html @@ -1,47 +1,47 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser hic Track Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>hic Track Format</h1> +<p><b>Note:</b> The UCSC tools currently support hic versions 6-8. +The <a target="_blank" href="hgHicTrackHelp.html">hic track configuration</a> help page +describes hic display options. +</p> <p> <a href="https://github.com/aidenlab/juicer/wiki/Data/#hic-files" target="_blank">Hic format</a> is an indexed binary format designed to permit fast random access to contact matrix heatmaps. The format was designed by the <a href="https://www.aidenlab.org/" target="_blank">Aiden Lab</a> at <a href="https://www.bcm.edu/" target="_blank">Baylor College of Medicine</a>. More information on the hic format itself can be found in the documentation on <a href="https://github.com/aidenlab/juicer/wiki/Data/#hic-files" target="_blank">Github</a>. </p> <p> The format is used for displaying chromatin conformation data in the browser. This format is useful for displaying interactions at a scale and depth that exceeds what can be easily visualized with the interact and bigInteract formats. After running a chromatin conformation experiment such as <em>in situ</em> Hi-C, researchers can pass their results through the <a href="https://github.com/aidenlab/juicer/wiki" target="_blank">Juicer</a> pipeline to produce a hic file. Due to the large size of many of these files, UCSC is not able to support direct upload via our Custom Track interface. Instead, users should place their Hic files in a web-accessible space and enter the URL as a bigDataUrl. If you do not have access to a web-accessible server and need hosting space for your Hic files, please see the <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub Help documentation.</p> -<p>The UCSC tools currently support hic versions 6-8. -The <a target="_blank" href="hgHicTrackHelp.html">hic track configuration</a> help page -describes hic display options. -</p> <div class='text-center'> <img src="../../images/hicDrawModes.png" alt="hic draw modes"> </div> <h2>Generating a hic track</h2> <p> The typical workflow for generating a hic custom track is this:</p> <ol> <li> Prepare your data by processing it with the <a href= "https://github.com/aidenlab/juicer/wiki" target="_blank">Juicer</a> pipeline to create a file in the hic format. </li> <li> Move the hic file (<em>my.hic</em>) to an http, https, or ftp location.</li> <li>