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 @@ -1,132 +1,135 @@ <!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> <pre><code>net chr2L 23011544 fill 6004 3278 chrXR_group3a - 1396397 2164 id 25606 score 23114 ali 782 qDup 576 type top tN 0 qN 0 tR 36 qR 0 tTrf 0 qTrf 0 gap 6065 2 chrXR_group3a - 1398498 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 6096 1485 chrXR_group3a - 1397572 897 tN 0 qN 0 tR 36 qR 0 tTrf 0 qTrf 0 fill 6096 513 chrU - 5570675 533 id 48675 score 4435 ali 465 qDup 533 type nonSyn tN 0 qN 0 tR 0 qR 13 tTrf 0 qTrf 0 gap 6116 8 chrU - 5571188 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 6156 5 chrU - 5571156 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 6184 3 chrU - 5571133 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 6212 18 chrU - 5571106 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 6244 9 chrU - 5571092 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 6340 2 chrU - 5570996 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 6515 3 chrU - 5570771 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7623 1 chrXR_group3a - 1397530 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7664 1007 chrXR_group3a - 1397008 482 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 fill 7664 382 chrXL_group1e - 8262003 506 id 25608 score 10609 ali 364 qDup 506 type nonSyn tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7784 4 chrXL_group1e - 8262361 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7792 3 chrXL_group1e - 8262357 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7921 2 chrXL_group1e - 8262126 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 7949 9 chrXL_group1e - 8262092 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 8693 1 chrXR_group3a - 1396985 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 fill 9833 1251 chrU - 5562980 1239 id 48675 score 10720 ali 1124 qDup 1094 type top tN 0 qN 0 tR 22 qR 88 tTrf 0 qTrf 0 gap 9966 7 chrU - 5564075 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 10015 3 chrU - 5564030 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 10088 2 chrU - 5563957 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 gap 10101 8 chrU - 5563946 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0 </code></pre> <h2>Field definitions</h2> <p> The net file consists of 7 fixed fields and a set of optional name/value pair fields. In the descriptions below, <em>target</em> refers to the reference species and <em>query</em> refers to the aligning species.</p> <h3>Fixed fields</h3> <ul> <li> <strong><em>Class</em></strong> -- Either <em>fill</em> or <em>gap</em>. Fill refers to a portion of a chain</li> <li> <em><strong>Start in chromosome</em></strong> -- (target species)</li> <li> <em><strong>Size</em></strong> -- target species)</li> <li> <em><strong>Chromosome name</em></strong> -- (query species)</li> <li> <em><strong>Relative orientation</em></strong> -- between target and query species</li> <li> <em><strong>Start in chromosome</em></strong> -- (query species)</li> <li> <em><strong>Size</em></strong> -- (query species)</li> </ul> <h3>Optional fields (Name/value pairs)</h3> <ul> <li> <em><strong>id</strong></em> -- ID of associated chain (gapped alignment), if any.</li> <li> <em><strong>score</strong></em> -- Score of associated chain.</li> <li> <em><strong>ali</strong></em> -- Number of bases in alignments in chain.</li> <li> <em><strong>qFar</strong></em> -- For fill that is on the same chromosome as parent, how far fill is from position predicted by parent. This helps determine if a rearrangement is local or if a duplication is tandem.</li> <li> <em><strong>qOver</strong></em> -- Number of bases overlapping with parent gap on query side. Generally, this will be near zero, except for inverts.</li> <li> <em><strong>qDup</strong></em> -- Number of bases in query region that are used twice or more in net. This helps distinguish between a rearrangement and a duplication.</li> <li> <em><strong>type</em></strong> -- One of the following values: <ul> <li> <em>top</em> -- Chain is top-level, not a gap filler.</li> <li> <em>syn</em> -- Chain is on same chromosome and in same direction as parent.</li> <li> <em>inv</em> -- Chain is on same chromosome on opposite direction from parent.</li> <li> <em>nonSyn</em> -- Chain is on a different chromosome from parent.</li> </ul> <li> <em><strong>tN</strong></em> -- Number of unsequenced bases (<em>N</em>s) on target side.</li> <li> <em><strong>qN</strong></em> -- Number of unsequenced bases on query side.</li> <li> <em><strong>tR</strong></em> -- Number of bases in RepeatMasker masked repeats on target.</li> <li> <em><strong>qR</strong></em> -- Number of bases in RepeatMasker masked repeats on query.</li> <li> <em><strong>tNewR</strong></em> -- Bases in lineage-specific repeats on target.</li> <li> <em><strong>qNewR</strong></em> -- Bases in lineage-specific repeats on query.</li> <li> <em><strong>tOldR</strong></em> -- Bases in repeats predating split on target.</li> <li> <em><strong>qOldR</strong></em> -- Bases in repeats predating split on query.</li> <li> <em><strong>tTrf</strong></em> -- Bases in trf (Tandem Repeat Finder) repeats on target.</li> <li> <em><strong>qTrf</strong></em> -- Bases in trf repeats on query.</li> </ul> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->