f60458991e24e246fd061ca1d4e6861585b0cd09 dschmelt Mon Apr 8 15:14:12 2019 -0700 Fixing minor things for code review #23271 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index d5f405b..8e1c758 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -203,31 +203,31 @@ 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> <h3>Example #4</h3> <p>In this example, you will convert a genePred file to bigGenePred using command line utilities. You can download utilities from the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utilities directory</a>.</p> <ol> <li> - Obtain a genePred extended file. Here we are downloading the Comprehensive Gencode V28 gene data. + Obtain a genePred extended file. In this example, we are downloading the Comprehensive Gencode V28 gene data. <pre><code>wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgEncodeGencodeCompV28.txt.gz</code></pre></li> <li> Uncompress the file. <pre><code>gunzip wgEncodeGencodeCompV28.txt.gz </code></pre></li> <li> Isolate columns 2 till the end, removing the bin column, and saving as <em>wgCompV28Cut.txt</em>. <pre><code>cut -f 2- wgEncodeGencodeCompV28.txt > wgCompV28Cut.txt </code></pre></li> <li> Convert the genePred extended file to a bigGenePred text file, reordering and adding columns. <pre><code>genePredToBigGenePred wgCompV28Cut.txt wgEncodeGencodeCompV28BigGP.txt</code></pre></li> <li> Obtain input files for the binary conversion. <pre><code>fetchChromSizes hg38 > hg38.chrom.sizes wget https://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bigGenePred.as</code></pre></li> <li>