1a02f1ea718003c05a9e29bd233029a81fc68bc5 dschmelt Thu Jul 9 15:45:26 2020 -0700 Clarifying baseColorDefault #25868 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index 60ab3d5..8346a35 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -129,52 +129,57 @@ <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 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</h3> +<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 codons and -amino acid numbering: +In this example, you will configure the bigGenePred track loaded in Example #1 to display +amino acids and codon numbering: <ol> <li> - On the bottom of the gene details page, click the "Go to User Track track controls" link.</li> + Access the track configuration page by right-clicking track and clicking + "Configure User Track" or alternately, from + the bottom of a gene's details page, click the "Go to User Track track + controls" link.</li> <li> - Change the "Color track by codons:" option from "OFF" to "genomic - codons" and change the display mode to "full". Then click - <button>Submit</button>. + Making sure the display is in pack or full, 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 controls page and click the box next to "Show codon numbering", + 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 numbering.</li> + letters and codon numbering when sufficiently zoomed in.</li> </ol> <p> -Alternatively, you can also add a parameter in the custom track line, <code>baseColorDefault=genomicCodons</code>, -to set amino acids to display by default:</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> <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 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: Bed12+8 to BigGenePred</h3> <p> In this example, you will create your own bigGenePred file from an existing pre-bigGenePred input file, a bed12+8 file.</p> <ol>