4ac05a32376cf48f5294c4aaeb9b056a527b0e31 dschmelt Wed Apr 10 13:34:47 2019 -0700 Adding anchors to examples for easier reference #21582 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index 5cf8820..8f3d8d8 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -107,57 +107,58 @@ Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. Note that any of the track attributes listed <a href="customTrack.html#TRACK">here</a> are applicable to tracks of type bigBed. The basic version of the track line will look something like this:</p> <pre><code>track type=bigGenePred name="My Big GenePred" description="A Gene Set Built from Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigGenePred.bb</code></pre> <p> <strong>Step 7.</strong> Paste this custom track line into the text box on the <a href="../../cgi-bin/hgCustom">custom track management page</a>.</p> <p> The <code>bedToBigBed</code> program can be run with several additional options. For a full list of the available options, type <code>bedToBigBed</code> (with no arguments) on the command line to display the usage message.</p> <h2>Examples</h2> +<a name="Example1"></a> <h3>Example #1</h3> <p> In this example, you will create a bigGenePred custom track using a bigGenePred file located on the UCSC Genome Browser http server, <em>bigGenePred.bb</em>. This file contains data for the hg38 assembly.</p> <p> To create a custom track using this bigGenePred file: <ol> <li> Construct a track line that references the hosted file:</p> <pre><code>track type=bigGenePred name="bigGenePred Example One" description="A bigGenePred file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb</code></pre> <li> Paste the track line into the <a href="../../cgi-bin/hgCustom?db=hg38">custom track management page</a> for the human assembly hg38 (Dec. 2013).</li> <li> Click the <button>Submit</button> button.</li> </ol> <p> Custom tracks can also be loaded via one URL line. The link below loads the same bigGenePred track and sets additional parameters in the URL:</p> <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb" target="_blank"><pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb</code></pre></a> <p> After this example bigGenePred track is loaded in the Genome Browser, click on a gene in the browser's track display to view the details page for that gene. Note that the page offers links to several sequence types, including translated protein, predicted mRNA, and genomic sequence.</p> - +<a name="Example2"></a> <h3>Example #2</h3> <p> In this example, you will configure the bigGenePred track loaded in Example #1 to display codons and amino acid numbering: <ol> <li> On the bottom of the gene details page, click the "Go to ... track controls" link.</li> <li> Change the "Color track by codons:" option from "OFF" to "genomic codons" and check that the display mode is set to "full". Then click <button>Submit</button>. <li> On the Genome Browser tracks display, zoom to a track region where amino acids display, such as <code>chr9:133,255,650-133,255,700</code>, and note that the track now displays codons. <li> @@ -166,61 +167,62 @@ <li> The browser tracks display will now show amino acid numbering.</li> </ol> <p> You can also add a parameter in the custom track line, <code>baseColorDefault=genomicCodons</code>, to set display codons by default:</p> <pre><code>browser position chr10:67,884,600-67,884,900 track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Two" description="A bigGenePred file" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb </code></pre> <p> Paste the above into the hg38 <a href="../../cgi-bin/hgCustom?db=hg38">custom track management page</a> to view an example of bigGenePred amino acid display at the beginning of the SIRT1 gene on chromosome 10.</p> <p class='text-center'> <img class='text-center' src="../../images/codonColoring.png" alt="An image of a track with codons colored" width="999"> </p> +<a name="Example3"></a> <h3>Example #3</h3> <p> In this example, you will create your own bigGenePred file from an existing bigGenePred input file.</p> <ol> <li> Save the example bed12+8 input file to your computer, <em><a href="examples/bigGenePred.txt">bigGenePred.txt</a></em>.</li> <li> Download the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/"><code>bedToBigBed</code></a> utility (<em>Step 2</em>, in the <em>Creating a bigGenePred</em> section above).</li> <li> Save the <a href="hg38.chrom.sizes"><em>hg38.chrom.sizes</em> text file</a> to your computer. This file contains the chrom.sizes for the human hg38 assembly (<em>Step 3</em>, above).</li> <li> Save the autoSql file <a href="examples/bigGenePred.as"><em>bigGenePred.as</em></a> to your computer.</li> <li> Run the <code>bedToBigBed</code> utility to create the bigGenePred output file (<em>step 4</em>, above): <pre><code><B>bedToBigBed</B> -type=bed12+8 -tab -as=bigGenePred.as bigGenePred.txt hg38.chrom.sizes bigGenePred.bb</code></pre></li> <li> Place the newly created bigGenePred file (<em>bigGenePred.bb</em>) on a web-accessible server (<em>Step 5</em>, above).</li> <li> Construct a track line that points to the bigGenePred file (<em>Step 6</em>, above).</li> <li> Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (<em>step 7</em>, above).</li> </ol> - +<a name="Example4"></a> <h3>Example #4</h3> <p>In this example, you will convert a GTF file to bigGenePred using command line utilities. You can download utilities from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utilities directory</a>.</p> <ol> <li> Obtain a GTF file using the wget command. Skip this step if you already have a GTF file. <pre><code>wget http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredExample4.gtf</code></pre></li> <li> Convert the GTF file to genePred extended format using the gtfToGenePred command. <pre><code>gtfToGenePred -genePredExt bigGenePredExample4.gtf example4.genePred</code></pre></li> <li> Convert the genePred extended file to a pre-bigGenePred text file. <pre><code>genePredToBigGenePred example4.genePred ex4BigGenePred.txt</code></pre></li> <li>