89c380d28049d3f28fd09a897260d1ee0fbb3248 dschmelt Mon Apr 29 15:32:09 2019 -0700 Making upper case Browser for code review #23399 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index 3397494..bc5537c 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -97,80 +97,80 @@ <p> <strong>Step 5.</strong> Move the newly created bigGenePred file (<em>myBigGenePred.bb</em>) to a web-accessible http, https, or ftp location. See <a href="hgTrackHubHelp.html#Hosting">hosting section</a> if necessary.</p> <p> <strong>Step 6.</strong> Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. Any of the track attributes will be available for use on bigBed tracks. 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 page</a> with your modified URL. Click <button>Submit</button> and your track should -load successfully. Then click <button>Go</button> to be taken to the browser window +load successfully. Then click <button>Go</button> to be taken to the Browser window with your custom track at the top. Note that there might not be data at all positions. </p> <h2>Examples</h2> <a name="Example1"></a> <h3>Example #1: Create a Custom Track</h3> <p> Create a bigGenePred custom track using the bigGenePred file located on the UCSC Genome Browser http server, <em>bigGenePred.bb</em>. This file contains data for the hg38 assembly.</p> <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 page</a> for the human assembly, hg38.</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 the track to -change display from dense to pack, then click on a gene in the browser's track display to view +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> <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 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>. <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", - then click <button>Submit</button>. The browser tracks display will now show amino acid + then click <button>Submit</button>. The Browser tracks display will now show amino acid letters and numbering.</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> <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> @@ -238,31 +238,31 @@ <a href="https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Hosting">hosting section</a> for more information.</li> <li> To view this example, you can click this into this Browser link. To view your own data, paste the link into your web browser and replace the URL after "bigDataUrl=" with a link to your own hosted data. <pre> <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr19:44905790-44909388&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredEx4.bb">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr19:44905790-44909388&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredEx4.bb</a></pre> You can also add your data in the <a href="../../cgi-bin/hgCustom?db=hg38">custom track management page</a>. This allows you to set position, configuration options, and write a more complete desciption. If you want to see codons, you can right click, then click configure codon view or set this options using <code>baseColorDefault=genomicCodons</code> as is done below. <pre><code>browser position chr19:44905790-44909388 track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Four" description="Ex4:BigGenePred Made from GTF" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePredEx4.bb</code></pre> Once you are done, you should have a track on the Genome Browser like the one below.</li> </ol> <p class='text-center'> - <img class='text-center' src="../../images/bigGenePredEx4.png" alt="An image of a bigGenePred track on the browser" width="999"> + <img class='text-center' src="../../images/bigGenePredEx4.png" alt="An image of a bigGenePred track on the Browser" width="999"> </p> <h2>Sharing your data with others</h2> <p> If you would like to share your bigGenePred data track with a colleague, learn how to create a URL link to your data by looking at <a href="customTrack.html#EXAMPLE6">Example #6</a> on the custom track help page.</p> <h2>Extracting data from bigBed format</h2> <p> Because the bigGenePred files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> <ul> <li>