b94d44b6a0b2fe7a114ba6ba04a0831cd674fed3 dschmelt Thu Jun 13 17:00:27 2019 -0700 minor wording changes #15449 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index a2a3db7..babffcd 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -242,59 +242,61 @@ <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"> </p> <a name="Example5"></a> <h3>Example #5: Create a BigGenePred Track Hub</h3> <p>In this example, you will set up a Track Hub that displays bigGenePred data and uses one of the -bigGenePred-specific settings to display gene codons. For more instruction on bigGenePred track -hubs, please visit the <a href=examples/hubExamples/hubBigGenePred/hg38/bigGenePredEHub.html> -bigGenePred example description page</a>. For complete instructions on Track Hubs, visit +bigGenePred-specific settings to display gene codon. For complete instructions on Track Hubs, visit the <a href=hgTrackHubHelp.html#Setup>Track Hub set-up page</a>.</p> <ol> <li>Make sure you have access to a web-hosted file location like GitHub, CyVerse, or an institutional website. This is where you will store your bigData files and configuration files. For more information, please visit the <a href=hgTrackHubHelp.html#Hosting>hosting section</a> of our Track Hub help guide.</li> <li>Copy the text from the <a href=examples/hubExamples/hubBigGenePred/>bigGenePred example hub files </a>into files on your hosting website. You will need a hub.txt and a genomes.txt file, along with a directory for each assembly you would like to display data on (e.g., hg38). Within your assembly directory, you will need your data file(s), (e.g., bigGenePredEHub.bb). Then you will need a trackDb.txt file which will define your track settings, such as the setting that displays genomic codons and amino acid letters, <code>baseColorDefault genomicCodons</code>.</li> -<li>Verify that you have the four required files in the following structure, where <strong>hg38</strong> is a directory: +<li>Verify that you have the four required files in the following structure, where +<strong>hg38</strong> is a directory: </br> --<a href=examples/hubExamples/hubBigGenePred/hub.txt>hub.txt</a></br> --<a href=examples/hubExamples/hubBigGenePred/genomes.txt>genomes.txt</a></br> <strong>--<a href=examples/hubExamples/hubBigGenePred/hg38/>hg38</a></strong></br> ----<a href=examples/hubExamples/hubBigGenePred/hg38/trackDb.txt>trackDb.txt</a></br> -----<a href=examples/hubExamples/hubBigGenePred/hg38/bigGenePred.bb>bigGenePred.bb</a></br> +----<a href=examples/hubExamples/hubBiigGenePred/hg38/bigGenePred.bb>bigGenePred.bb</a></br> +You may also include a hub description page and a +<a href=examples/hubExamples/hubBigGenePred/hg38/bigGenePredEHub.html>track description page</a>, +where you will find additional instructions. </li> <li>Copy the link to your hub.txt file URL of your hub.txt file and paste it into the text input box on the <a href=../../../cgi-bin/hgHubConnect>Track Hub page.</a> For an example, you can paste the following link into the input box: <a href=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubBigGenePred/hub.txt> http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubBigGenePred/hub.txt</a>. -This should connect you to your hub, with the data available by navagating to your +This should connect you to your hub, with the data available by navigating to your assembly of interest.</li> <p class='text-center'> <img class='text-center' src="../../images/bigGenePredHub.png" alt="An image of a bigGenePred track hub on the Browser" width="999"> </p> </ol> <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