8b76506ec11f2a1bd3bbdae4e27afa7894754dfc
dschmelt
  Wed Apr 10 17:10:34 2019 -0700
Changing example4 #21582

diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html
index 8f3d8d8..92942be 100755
--- src/hg/htdocs/goldenPath/help/bigGenePred.html
+++ src/hg/htdocs/goldenPath/help/bigGenePred.html
@@ -201,62 +201,63 @@
   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 &num;4</h3>
 <p>In this example, you will convert a GTF file to bigGenePred using command line utilities.
-You can download utilities from the
+You will need <em>gtfToGenePred</em>, <em>genePredTobigGenePred</em>,
+and <em>bedToBigBed</em>. 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>
+  <pre><code>genePredToBigGenePred example4.genePred bigGenePred.txt</code></pre></li>
   <li>
   Obtain helper files for the conversion from pre-bigGenePred to binary bigGenePred.
-  <pre><code>fetchChromSizes hg38 > hg38.chrom.sizes
+  <pre><code>wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
 wget http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.as</code></pre></li>
   <li>
   Convert your text bigGenePred to a binary indexed format.
-  <pre><code>bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as ex4BigGenePred.txt hg38.chrom.sizes ex4BigGenePred.bb</code></pre></li>
+  <pre><code>bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as ex4BigGenePred.txt hg38.chrom.sizes bigGenePred.bb</code></pre></li>
   <li> 
   Put your binary indexed file in a web-accessible location. See the 
   <a href=”https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Hosting”>hosting section</a> for more information.</li>
   <li>
   View your dataset in the Browser by entering your hosted data URL in the bigDataUrl field of the 
   URL. For example, you can paste this link into your web browser.
-  <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/ex4bigGenePred.bb</code></pre>
+<pre> <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">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.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 these options using the <code>baseColorDefault=genomicCodons</code> code as is done below.
-<pre><code>browser position chr10:67,884,600-67,884,900 
-track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Four" description="BGP Made from genePred" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/ex4bigGenePred.bb</code></pre></li>
+<pre><code>browser position chr19:44905795-44909393 
+track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Four" description="BGP Made from genePred" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb</code></pre></li>
 </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>.</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 
   <code>bigBedToBed</code> &mdash; converts a bigBed file to ASCII BED format.</li>
   <li>
   <code>bigBedSummary</code> &mdash; extracts summary information from a bigBed 
   file.</li>