a729a9e1d69997979c922c69f1cfb0f55cd5fe98 brianlee Sat Jun 25 07:49:13 2022 -0700 Expanding an example on trix.html, no RM diff --git src/hg/htdocs/goldenPath/help/trix.html src/hg/htdocs/goldenPath/help/trix.html index 464d4c7..08d18ec 100755 --- src/hg/htdocs/goldenPath/help/trix.html +++ src/hg/htdocs/goldenPath/help/trix.html @@ -1,44 +1,63 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Trix Indices" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Trix Indices</h1> <p> A Trix index consists of a pair of files that allow for fast look-up of free text associated with a list of identifiers. The index is created from a single line-oriented text file using the program <code>ixIxx</code>. Each line in the text file starts with an identifier, followed by free text associated with the ID. For a more complete description of how to make a searchable track hub (or custom track), please visit the <a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable track hubs</a>.</p> <p> To complete the steps below you must first download the <code>ixIxx</code> utility. For more information on downloading our command line utilities, see these <a href="http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads">instructions</a>.</p> +<h3 id="ex1">Example 1</h3> <p> To create a Trix index, follow these steps: <ol> <li> Prepare a text file that associates your IDs with free text:<br> <pre><code> id1 this is text for id1 id2 this is text for id2 id3 this is text for id3</code></pre></li> <li> Run the <code>ixIxx</code> program on your text file.<br> <pre><code> ixIxx input.txt myTrix.ix myTrix.ixx</code></pre></li> </ol> +<h3 id="ex2">Example 2</h3> +<ol> + <li> + If you have a bigBed track with unique gene names such as + <code>SIRT1, BRCA1, TP53</code> in the fourth name + column, and you built the bigBed using the option of + <code>-extraIndex=name</code> to index the name field you can create an + input.txt such as the following that associates the bigBed name with other + identifiers people might search for or with shorter spellings of the names: + <pre> + SIRT1 sirt1 sir sirt SIR SIRT Sirtuin SIR2-Like ENSG00000096717 NM_012238 + BRCA1 brca1 brca brc BRC BRCA breast cancer 1 ENSG00000012048 NM_007300 + TP53 tp53 tp5 TP5 Tumor Protein P53 ENSG00000141510 NM_001126112</pre></li> + <li> + You would then run the <code>ixIxx</code> program on your text file.<br> + <pre><code> ixIxx input.txt myTrix.ix myTrix.ixx</code></pre></li> +</ol> + <h3 id="resources">Resources and examples</h3> <p> If you want to use your Trix index in a track hub, see the <code>searchTrix</code> setting in the <a href="trackDb/trackDbHub.html#searchTrix">Track Database Definition Document</a>.</p> <p> Review our <a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable track hubs</a> for illustrated steps building a track hub.</p> <p> There are also tools available for taking genePred format to trix format, such as this <a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/utils/automation/gpToIx.pl" target="_blank">gpToIx.pl</a> perl script.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->