198c9b8daecc44fbda6a6494c566c723920f030a
lrnassar
  Wed Mar 11 18:25:21 2026 -0700
Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.

diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html
index 603afa3a5f2..1695e8f97a1 100755
--- src/hg/htdocs/goldenPath/help/bigGenePred.html
+++ src/hg/htdocs/goldenPath/help/bigGenePred.html
@@ -220,67 +220,67 @@
   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: GTF (or GFF) to BigGenePred </h3>
 <p>In this example, you will convert a GTF file to bigGenePred using command line utilities.
-You will need <code>gtfToGenePred</code>, <code>genePredTobigGenePred</code>,
+You will need <code>gtfToGenePred</code>, <code>genePredToBigGenePred</code>,
 and <code>bedToBigBed</code>. If you would like to convert a GFF file to bigGenePred, you will use
 <code>gff3ToGenePred</code> in place of the <code>gtfToGenePred</code>. You can download utilities from the
 <a href="http://hgdownload.gi.ucsc.edu/admin/exe/">utilities directory</a>.</p>
 <ol>
   <li>
   Obtain a GTF file using the <code>wget</code> command. Skip this step if you already have a GTF
   or GFF 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 <code>gtfToGenePred</code> command.
   <pre><code>gtfToGenePred -genePredExt bigGenePredExample4.gtf example4.genePred</code></pre>
   If you are converting a GFF file, use the <code>gff3ToGenePred</code> command.
   <pre><code>gff3ToGenePred yourFile.gff example4.genePred </pre></code></li>
   <li>
   Convert the genePred extended file to a pre-bigGenePred text file.
   <pre><code>genePredToBigGenePred example4.genePred bigGenePredEx4.txt</code></pre></li>
   <li>
   Download a helper file that specifies column names.
   <pre><code>wget https://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.as</code></pre>
   </li>
   <li>
   Convert your text bigGenePred to a binary indexed format. If you are not using hg38,
   you will need to replace the hg38.chrom.sizes file path with your organism's file path from the
   <a href="http://hgdownload.gi.ucsc.edu">downloads directory</a> under "Genome Sequence Files".
   <pre><code>bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as bigGenePredEx4.txt http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes bigGenePredEx4.bb</code></pre></li>
   <li> 
   Put your binary indexed file, bigGenePredEx4.bb, 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>
-  To view this example, you can click this into this Browser link. To view your own data, paste the
+  To view this example, you can click 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
+description. 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 &num;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. You can see a pre-built version of this hub
 by clicking 
 <a href="../../cgi-bin/hgTracks?db=hg38&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubBigGenePred/hub.txt">
 this link</a>.</p>
@@ -302,31 +302,31 @@
 </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>
 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 URL address of your hub.txt file and paste it into the text input box on the 
 <a href="../../../cgi-bin/hgHubConnect#unlistedHubs">Track Hub page</a>. For an example, 
 you can paste the following link into the input box: 
 <a href="examples/hubExamples/hubBigGenePred/hub.txt">
 http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubBigGenePred/hub.txt</a>.
-Clicking the <button>Add Hub</button> button will connect to your track hub and navagate you to 
+Clicking the <button>Add Hub</button> button will connect to your track hub and navigate you to 
 your assembly of interest. For more instructions on setting up Track Hubs, visit the 
 <a href="hgTrackHubHelp.html#Setup">Track Hub set-up page</a>.</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