4fcea62ede5b34df814333e242a865fb20dfb821 max Thu Dec 10 02:57:37 2020 -0800 adding linux commands to bigBed example 2, no redmine yet, but probably coming. diff --git src/hg/htdocs/goldenPath/help/bigBed.html src/hg/htdocs/goldenPath/help/bigBed.html index 059c9eb..d86e687 100755 --- src/hg/htdocs/goldenPath/help/bigBed.html +++ src/hg/htdocs/goldenPath/help/bigBed.html @@ -125,48 +125,62 @@ certain parameters: </p> <ol> <li> Construct a track line that references the <em>bigBedExample.bb</em> file: <pre><code>track type=bigBed name="bigBed Example One" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</code></pre></li> <li> Include the following browser line to ensure that the custom track opens at the correct position: <pre><code>browser position chr21:33,031,597-33,041,570</code></pre></li> <li> Paste the browser and track lines into the <a href="../../cgi-bin/hgCustom">custom track</a> management page, click the "submit" button, then click the "chr21" link in the custom track listing to view the bigBed track in the Genome Browser.</li> </ol> +<a name=Ex2></a> <h3>Example #2</h3> <p> In this example, you will create your own bigBed file from an existing bed file.</p> <ol> <li> - Save the BED file <a href="examples/bedExample.txt"><em>bedExample.txt</em></a> to your computer - (<em>Steps 1</em> and <em>2</em> in <em>Creating a bigBed track</em>, above).</li> + Save the BED file <a href="examples/bedExample.txt"><em>bedExample.txt</em></a> to a server, ideally one + that is accessible from the internet. + (<em>Steps 1</em> and <em>2</em> in <em>Creating a bigBed track</em>, above).<br> + <pre><code>wget https://genome.ucsc.edu/goldenPath/help/examples/bedExample.txt</code></pre> + </li> <li> Save the file <a href="hg19.chrom.sizes"><em>hg19.chrom.sizes</em></a> to your computer. It - contains the chrom.sizes data for the human (hg19) assembly (<em>Step 4</em>, above).</li> + contains the chrom.sizes data for the human (hg19) assembly (<em>Step 4</em>, above).<br> + <pre><code>wget https://genome.ucsc.edu/goldenPath/help/hg19.chrom.sizes</code></pre> + </li> <li> - Download the <code>bedToBigBed</code> utility (<em>Step 3</em>, above).</li> + Download the <code>bedToBigBed</code> utility (<em>Step 3</em>, above). Replace "linux" below with "macOSX" + if your server is a Mac. + <pre><code>wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed +chmod a+x bedToBigBed</code></pre> + </li> <li> Run the utility to create the bigBed output file (<em>Step 5</em>, above): <pre><code><strong>bedToBigBed</strong> bedExample.txt hg19.chrom.sizes myBigBed.bb</code></pre></li> <li> Place the bigBed file you just created (<em>myBigBed.bb</em>) on a web-accessible server - (<em>Step 6</em>, above).</li> + (<em>Step 6</em>, above).<br> + <pre><code>mv myBigBed.bb ~/public_html/</code></pre> + At some Universities, this involves using the commands ftp, scp or rsync to copy the file to a different server, one that is accessible + from the internet. We have <a href="hgTrackHubHelp.html#Hosting">documentation</a> how to find such a server. + </li> <li> Paste the URL itself into the Custom Tracks entry form or construct a track line that points to your bigBed file (<em>Step 7</em>, above).</li> <li> Create the custom track on the human assembly hg19 (Feb. 2009), and view it in the Genome Browser (<em>Step 8</em>, above). Note that the original BED file contains data on chromosome 21 only.</li> </ol> <a name=Ex3></a> <h3>Example #3</h3> <p> In this example, you will create your own bigBed file from a fully featured existing BED file that contains the standard BED fields up to and including the <em>color</em> field (field 9), plus two additional non-standard fields (two alternate names for each item in the file). Since the resulting