bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/net.html src/hg/htdocs/goldenPath/help/net.html index 3a6f3478c14..9e359055a9a 100755 --- src/hg/htdocs/goldenPath/help/net.html +++ src/hg/htdocs/goldenPath/help/net.html @@ -1,28 +1,28 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Net Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Net Format</h1> <p> The <em>net</em> file format is used to describe the axtNet data that underlie the net alignment annotations in the Genome Browser. For a detailed description of the methods used to generate these data, refer to the Genome Browser description pages that accompany the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">downloadable net alignment tracks</a>. +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">downloadable net alignment tracks</a>. You can find a detailed <a href="https://genomewiki.ucsc.edu/index.php?title=Chains_Nets#Net_construction_example" target="_blank">example</a> how nets are constructed on our wiki.</p> <p> At the beginning of each target species chromosome, a "net" line appears with the format:</p> <pre><code>net chromName chromSize</code></pre> <p> <em>chromName</em> is the target species chromosome name, and <em>chromSize</em> is the chromosome size. For example:</p> <pre><code>net chr2L 23011544</code></pre> <p> Each target chromosome section in the file starts with a net line. The net line is followed by a set of "fill" and "gap" lines.</p> <p>