2702c32c069eb7e3ec51beb22d1d160a6538e6d2 dschmelt Mon Jul 13 17:09:05 2020 -0700 Code review refs #25875 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index 8346a35..1f92ddd 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -135,36 +135,37 @@ <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 the track to change display from dense to pack, then click on a gene in the Browser's track display to view the gene details page. Note that the page offers links to translated protein, predicted mRNA, and genomic sequence.</p> <a name="Example2"></a> <h3>Example #2: Display Amino Acids and Codon Numbers</h3> <p> In this example, you will configure the bigGenePred track loaded in Example #1 to display amino acids and codon numbering: <ol> <li> - Access the track configuration page by right-clicking track and clicking + Access the track configuration page by right-clicking anywhere in the track and clicking "Configure User Track" or alternately, from - the bottom of a gene's details page, click the "Go to User Track track + within a gene's details page, click the "Go to User Track track controls" link.</li> <li> - Making sure the display is in pack or full, change the "Color track by codons:" + Making sure the display is in pack or full visibility mode, change the "Color + track by codons:" option from "OFF" to "genomic codons". Then click <button>Submit</button> or <button>Ok</button>.</li> <li> Zoom to a region with track data, such as <code>chr9:133,255,650-133,255,700</code>, and note that the track now displays amino acids. <li> Return to the track configuration page and check the box next to "Show codon numbering", then click <button>Submit</button>. The Browser tracks display will now show amino acid letters and codon numbering when sufficiently zoomed in.</li> </ol> <p> Alternatively, you can also add a parameter in the custom track line, <strong><code>baseColorDefault=genomicCodons</code></strong>, to set amino acids and codon numbering to display by default:</p>