b089078d975056489840af38badc2598592bc47f dschmelt Mon Apr 15 14:15:57 2019 -0700 Fixing weird double quotes character #23317 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index ec79cb3..d911d7e 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -223,31 +223,31 @@ <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 bigGenePred.txt</code></pre></li> <li> Obtain helper files for the conversion from pre-bigGenePred to binary bigGenePred. <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 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> + <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> <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 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>