f3b875cc2d7a6c152370f9347de35505438e8fd5 dschmelt Mon Apr 15 13:56:50 2019 -0700 Changed minor things for code review #23317 diff --git src/hg/htdocs/goldenPath/help/bigGenePred.html src/hg/htdocs/goldenPath/help/bigGenePred.html index 92942be..ec79cb3 100755 --- src/hg/htdocs/goldenPath/help/bigGenePred.html +++ src/hg/htdocs/goldenPath/help/bigGenePred.html @@ -128,32 +128,32 @@ <p> To create a custom track using this bigGenePred file: <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 (Dec. 2013).</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> +<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgct_customText=track&type=bigGenePred&bigDataUrl=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&type=bigGenePred&bigDataUrl=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 a gene in the browser's track display to view the details page for that gene. Note that the page offers links to several sequence types, including translated protein, predicted mRNA, and genomic sequence.</p> <a name="Example2"></a> <h3>Example #2</h3> <p> In this example, you will configure the bigGenePred track loaded in Example #1 to display codons and amino acid numbering: <ol> <li> On the bottom of the gene details page, click the "Go to ... track controls" link.</li> <li> Change the "Color track by codons:" option from "OFF" to "genomic codons" and check that the display mode is set to "full". Then click @@ -245,30 +245,33 @@ 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> <h2>Extracting data from bigBed format</h2> <p> Because the bigGenePred files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the +<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> +<ul> + <li> <code>bigBedToBed</code> — converts a bigBed file to ASCII BED format.</li> <li> <code>bigBedSummary</code> — extracts summary information from a bigBed file.</li> <li> <code>bigBedInfo</code> — prints out information about a bigBed file.</li> </ul> <p> As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the command line to view the usage statement.</p> <h2>Troubleshooting</h2> <p> If you encounter an error when you run the <code>bedToBigBed</code> program, check your input file for data coordinates that extend past the end of the chromosome. If these are