e2f1d4f8b6309f36a64c62fd87a85434811b05f3
dschmelt
  Tue Sep 10 09:33:46 2019 -0700
Adding hard link to save users 1 command in bedToBigBed conversion #24092

diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html
index ea1eca6..60ab3d5 100755
--- src/hg/htdocs/goldenPath/help/bigGenePred.html
+++ src/hg/htdocs/goldenPath/help/bigGenePred.html
@@ -212,40 +212,40 @@
 <a href="http://hgdownload.soe.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>
-  Obtain helper files for the conversion to binary bigGenePred. If you are not using hg38, 
-  you can find the chrom.sizes file for your organism in the
-  <a href="http://hgdownload.soe.ucsc.edu">downloads directory</a> under "Full data set".
-  <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>
+  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.
-  <pre><code>bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as bigGenePredEx4.txt hg38.chrom.sizes bigGenePredEx4.bb</code></pre></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.soe.ucsc.edu">downloads directory</a> under "Genome Sequence Files".
+  <pre><code>bedToBigBed -type=bed12+8 -tab -as=bigGenePred.as bigGenePredEx4.txt http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes bigGenePredEx4.bb</code></pre></li>
   <li> 
-  Put your binary indexed file in a web-accessible location. See the 
+  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
   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'>