947a8b9ea2a461b1a92629306de66e995d557c32 dschmelt Tue Apr 23 11:21:26 2019 -0700 Finishing cut off sentence, adding code tags in Ex4 #23354 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index ec10044..3397494 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -96,46 +96,49 @@ <pre><code><strong>bedToBigBed</strong> -as=bigGenePred.as -type=bed12+8 bigGenePred.txt chrom.sizes myBigGenePred.bb</code></pre> <p> <strong>Step 5.</strong> Move the newly created bigGenePred file (<em>myBigGenePred.bb</em>) to a web-accessible http, https, or ftp location. See <a href="hgTrackHubHelp.html#Hosting">hosting section</a> if necessary.</p> <p> <strong>Step 6.</strong> Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. Any of the track attributes will be available for use on bigBed tracks. The basic version of the track line will look something like this:</p> <pre><code>track type=bigGenePred name="My Big GenePred" description="A Gene Set Built from Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigGenePred.bb</code></pre> <p> <strong>Step 7.</strong> Paste this custom track line into the text box on the <a href="../../cgi-bin/hgCustom">custom -track management page</a>. Click <button>Go</button> and you should be taken to a </p> +track page</a> with your modified URL. Click <button>Submit</button> and your track should +load successfully. Then click <button>Go</button> to be taken to the browser window +with your custom track at the top. Note that there might not be data at all positions. +</p> <h2>Examples</h2> <a name="Example1"></a> <h3>Example #1: Create a Custom Track</h3> <p> Create a bigGenePred custom track using the bigGenePred file located on the UCSC Genome Browser http server, <em>bigGenePred.bb</em>. This file contains data for the hg38 assembly.</p> <ol> <li> Construct a track line that references the hosted file:</p> <pre><code>track type=bigGenePred name="bigGenePred Example One" description="A bigGenePred file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb</code></pre> <li> - Paste the track line into the <a href="../../cgi-bin/hgCustom?db=hg38">custom track management - page</a> for the human assembly hg38.</li> + Paste the track line into the <a href="../../cgi-bin/hgCustom?db=hg38">custom track + page</a> for the human assembly, hg38.</li> <li> Click the <button>Submit</button> button.</li> </ol> <p> Custom tracks can also be loaded via one URL line. The link below loads the same bigGenePred track and sets additional parameters in the URL:</p> <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" target="_blank"><pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track%20type=bigGenePred%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb</code></pre></a> <p> After this example bigGenePred track is loaded in the Genome Browser, click on the track to change display from dense to pack, then click on a gene in the browser's track display to view the gene details page. Note that the page offers links to translated protein, predicted mRNA, and genomic sequence.</p> <a name="Example2"></a> @@ -152,31 +155,31 @@ <button>Submit</button>. <li> Zoom to a region with track data, such as <code>chr9:133,255,650-133,255,700</code>, and note that the track now displays amino acids. <li> Return to the track controls page and click the box next to "Show codon numbering", then click <button>Submit</button>. The browser tracks display will now show amino acid letters and numbering.</li> </ol> <p> Alternatively, you can also add a parameter in the custom track line, <code>baseColorDefault=genomicCodons</code>, to set amino acids to display by default:</p> <pre><code>browser position chr10:67,884,600-67,884,900 track type=bigGenePred baseColorDefault=genomicCodons name="bigGenePred Example Two" description="A bigGenePred file" visibility=pack bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.bb </code></pre> <p> -Paste the above into the hg38 <a href="../../cgi-bin/hgCustom?db=hg38">custom track management +Paste the above into the hg38 <a href="../../cgi-bin/hgCustom?db=hg38">custom track page</a> to view an example of bigGenePred amino acid display at the beginning of the SIRT1 gene on chromosome 10.</p> <p class='text-center'> <img class='text-center' src="../../images/codonColoring.png" alt="An image of a track with codons colored" width="999"> </p> <a name="Example3"></a> <h3>Example #3: Bed12+8 to BigGenePred</h3> <p> In this example, you will create your own bigGenePred file from an existing pre-bigGenePred input file, a bed12+8 file.</p> <ol> <li> Save the example bed12+8 input file to your computer, <em><a href="examples/bigGenePred.txt">bigGenePred.txt</a></em>.</li> <li> @@ -192,42 +195,43 @@ 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 #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 <em>gtfToGenePred</em>, <em>genePredTobigGenePred</em>, -and <em>bedToBigBed</em>. If you would like to convert a GFF file to bigGenePred, you will use -<em>gff3ToGenePred</em> in place of the <em>gtfToGenePred</em>. You can download utilities from the +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.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 or GFF file. + 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 gtfToGenePred command. + 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 gff3ToGenePred command. + 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> <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> <li> Put your binary indexed file in a web-accessible location. See the