00057db86302a9c69088b6f89ee6884b428754d1 dschmelt Mon Feb 14 10:59:56 2022 -0800 Fixing incorrect ordering and titles suggested by refs #28912 diff --git src/hg/htdocs/goldenPath/help/bigBed.html src/hg/htdocs/goldenPath/help/bigBed.html index 4f2f3f4..e13afcc 100755 --- src/hg/htdocs/goldenPath/help/bigBed.html +++ src/hg/htdocs/goldenPath/help/bigBed.html @@ -40,31 +40,31 @@ <pre><code>wget https://genome.ucsc.edu/goldenPath/help/examples/bedExample.txt wget https://genome.ucsc.edu/goldenPath/help/hg19.chrom.sizes wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed chmod a+x bedToBigBed ./bedToBigBed bedExample.txt hg19.chrom.sizes myBigBed.bb mv myBigBed.bb ~/public_html/ </code></pre> The last step assumes that your ~/public_html/ directory is accessible from the internet. This may not be the case on your server. You may have to copy the file to another server and web-accessible location at your University. Once you know the URL to the file myBigBed.bb, you can paste this URL into the <a href="../../cgi-bin/hgCustom">custom track</a> box on the UCSC Genome Browser to display the file. <a name=overview></a> -<h2>Overview of the steps to create a bigBed track</h2> +<h2>Creating a bigBed track</h2> <p> To create a bigBed track, follow these steps (for concrete Unix commands, see the examples below on this page):<p> <p> <strong>Step 1.</strong> Create a BED format file following the directions <a href="../../FAQ/FAQformat.html#format1">here</a>. When converting a BED file to a bigBed file, you are limited to one track of data in your input file; therefore, you must create a separate BED file for each data track. Your BED file must be sorted. <p> If your BED file was originally a custom track, remove any existing "track" or "browser" lines from your BED file so that it contains only data. Also the input BED must be sorted, performed with this command: <code>sort -k1,1 -k2,2n unsorted.bed > input.bed</code> </p> @@ -101,130 +101,131 @@ Use the <code>bedToBigBed</code> utility to create a bigBed file from your sorted BED file, using the <em>input.bed</em> file and <em>chrom.sizes</em> files created in <em>Steps 1</em> and <em>3</em>:</p> <pre><code><strong>bedToBigBed</strong> input.bed chrom.sizes myBigBed.bb</code></pre> <p> <strong>Step 5.</strong> Move the newly created bigBed file (<em>myBigBed.bb</em>) to a web-accessible http, https, or ftp location. At this point you should have a URL to your data, such as "https://institution.edu/myBigBed.bb", and the file should be accessible outside of your institution/hosting providers network. For more information on where to host your data, please see the <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub Help documentation.</p> <p> <strong>Step 6.</strong> If the file name ends with a <em>.bigBed</em> or <em>.bb</em> suffix, you can paste the URL of the file directly into the <a href="../../cgi-bin/hgCustom">custom track</a> management page, click "submit" and view the file as a track in the Genome Browser. By default, the file name will be used to name the track. To configure the track name and descriptions, you must create a "<a href="hgTracksHelp.html#TRACK">track -line</a>", as shown in <em>Step 8</em>.</p> +line</a>", as shown in Example 1 Configuration <em>Step 1</em>.</p> <p> Alternatively, if you want to set the track labels and other options yourself, construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single track line. Note that any of the track attributes listed <a href="customTrack.html#TRACK">here</a> are applicable to tracks of type bigBed. The most basic version of the track line will look something like this:</p> <pre><code><strong>track type=</strong>bigBed <strong>name=</strong>"My Big Bed" <strong>description=</strong>"A Graph of Data from My Lab" <strong>bigDataUrl=</strong>http://myorg.edu/mylab/myBigBed.bb</code></pre> <p> Paste this custom track line into the text box on the <a href="../../cgi-bin/hgCustom">custom track</a> management page.</p> <h2>Examples</h2> <a name=Ex1></a> <h3>Example #1: Load an existing bigBed file</h3> <p> In this example, you will load an existing bigBed file, -<em>bigBedExample.bb</em>, on the UCSC http server. This file contains chromosome 21 data on the +<em>bigBedExample.bb</em>, on the UCSC http server. This file contains data on chromosome 21 on the human hg19 assembly.</p> <p> To create a custom track using this bigBed file:</p> <ol> <li> Paste the URL <code>http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</code> into the <a href="../../cgi-bin/hgCustom?db=hg19">custom track</a> management page for the human assembly hg19 (Feb. 2009).</li> <li> Click the "submit" button. </li> <li> On the next page that displays, click the "go" link. To view the data in the bigBed track in the Genome Browser navigate to <code>chr21:33,031,597-33,041,570</code>.</li> </ol> +<h4>Configuration</h4> <p> -Alternatively, you can customize the track display by including track and browser lines that define +You can customize the track display by including track and browser lines that define 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> +<pre>track type=bigBed name="bigBed Example One" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</pre></li> <li> Paste the track line into the <a href="../../cgi-bin/hgCustom?db=hg19">custom track</a> management page, click the "submit" button. On the next page that displays, click the "go" link. To view the data in the bigBed track in the Genome Browser navigate to <code>chr21:33,031,597-33,041,570</code>.</li> <li> With the addition of the following browser line with the track line you can ensure that the custom track opens at the correct position when you paste in the information: <pre><code>browser position chr21:33,031,597-33,041,570 track type=bigBed name="bigBed Example One" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb</code></pre> Paste the browser and track lines into the <a href="../../cgi-bin/hgCustom?db=hg19">custom track</a> page, click the "submit" button and the "go" link to see the data.</li> </ol> <a name=Ex2></a> <h3>Example #2: Create a bigBed file from a BED file</h3> <p> In this example, you will convert a sample BED file to bigBed format.</p> <ol> <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).<br> + contains the chrom.sizes data for the human (hg19) assembly (<em>Step 3</em>, above).<br> <pre><code>wget https://genome.ucsc.edu/goldenPath/help/hg19.chrom.sizes</code></pre> </li> <li>If you use your own file, it has to be sorted, first on the <code>chrom</code> field, and secondarily on the <code>chromStart</code> field. You can use the utility <code>bedSort</code> available <a href="http://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">here</a> or the following UNIX <code>sort</code> command to do this: </p> <pre><code>sort -k1,1 -k2,2n unsorted.bed > input.bed</code></pre> </li> <li> - Download the <code>bedToBigBed</code> utility (<em>Step 3</em>, above). Replace "linux" below with "macOSX" + Download the <code>bedToBigBed</code> utility (<em>Step 2</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): + Run the utility to create the bigBed output file (<em>Step 4</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).<br> + (<em>Step 5</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> + points to your bigBed file (<em>Step 5</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 + (<em>Step 6</em>, above). Note that the original BED file contains data on chromosome 21 only.</li> </ol> <a name=Ex3></a> <h3>Example #3: Create a bigBed file with extra (custom) fields</h3> <p> BigBed files can store extra fields in addition to the <a href="../../FAQ/FAQformat.html#format1">predefined BED fields</a>. 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 called <em>itemRgb</em> (field 9), plus two additional non-standard fields (two alternate names for each item in the file). The standard BED column itemRgb contains an R,G,B color value (e.g. "255,0,0"). The resulting