048b2becc526e0ec8ef7d4a172543349e72d2020 mspeir Mon Jan 27 10:00:50 2025 -0800 adding pointers to net construction example in GenomeWiki, refs #26358 diff --git src/hg/htdocs/goldenPath/help/net.html src/hg/htdocs/goldenPath/help/net.html index af55364d1e9..f78389063c5 100755 --- src/hg/htdocs/goldenPath/help/net.html +++ src/hg/htdocs/goldenPath/help/net.html @@ -1,28 +1,31 @@ <!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>.</p> +<a href="http://hgdownload.soe.ucsc.edu/downloads.html">downloadable net alignment tracks</a>. +You can find 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> <strong>File indentation:</strong> Line indentation level represents the parent/child relationship between records and is a necessary part of the net file format. Child records are indented one space from the parent, as shown in the example net file below.</p>