b7d562f6d2b90c3755c508c1a5b98c67648bf5b9 brianlee Tue Nov 17 14:16:52 2020 -0800 Working with Gerardo to resolve a git merge on bigLolly.html and adding some </li> and punctuation changes after running htmlCheck validate on the page refs #26481 diff --git src/hg/htdocs/goldenPath/help/bigLolly.html src/hg/htdocs/goldenPath/help/bigLolly.html index 9e7980c..531fd30 100755 --- src/hg/htdocs/goldenPath/help/bigLolly.html +++ src/hg/htdocs/goldenPath/help/bigLolly.html @@ -36,104 +36,94 @@ <p> In this example, you will create a bigLolly custom track using an existing bigBed file, located on the UCSC Genome Browser http server. By default the score field is used to define the lollipop height. This file contains data for the hg38 assembly.</p> <p> To create a custom track using this bigBed file: <ol> <li> Construct a track line that references the file:</p> <pre><code>track type=bigLolly name="bigLolly Example One" description="A bigLolly file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample3.bb visibility=full</code></pre></li> <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 "submit" button.</li> <li> - Go to chr21:17,030,007-17,055,589 to see the data. + Go to chr21:17,030,007-17,055,589 to see the data.</li> </ol> <p> <!-- FIX ME --> Custom tracks can also be loaded via one URL line. <a href="../../cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:17,002,145-17,159,243&hgct_customText=track%20type=bigLolly%20name=Example%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample3.bb%20visibility=pack" target="_blank">This link</a> loads the same <em>bigLolly.bb</em> track and sets additional display parameters in the URL:</p> -<pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:17,002,145-17,159,243&hgct_customText=track%20type=bigLolly%20name=Example %20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample3.bb %20visibility=full</a></code></pre> +<pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:17,002,145-17,159,243&hgct_customText=track%20type=bigLolly%20name=Example %20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample3.bb %20visibility=full</code></pre> <p> <h3>Example #2</h3> <p> In this example, you will create your own bigBed file to display as a bigLolly from an bed file, using an extra field to define the height of the lollipops.</p> <ol> <li> Save <a href="examples/bigLollyExample2.bed">this bed file</a> to your computer.</li> <li> - Save the autoSql files <a href="examples/bigLollyExample2.as"><em>bigLollyExample2.as</em></a> and + Save the autoSql files <a href="examples/bigLollyExample2.as"><em>bigLollyExample2.as</em></a> to your computer.</li> <li> Download the <code>bedToBigBed</code> <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utility</a>.</li> <li> Save the <a href="hg38.chrom.sizes"><em>hg38.chrom.sizes</em> text file</a> to your computer. This file contains the chrom.sizes for the human hg38 assembly.</li> <li> Use the <code>bedToBigBed</code> utility to create a bigBed file from your sorted BED file, using the <em>bigLollyExample2.bed</em> file and <em>chrom.sizes</em> files created above. </p> -<pre><code><strong>bedToBigBed</strong> -as=bigLollyExample2.as -type=bed9+1 bigLollyExample2.bed hg38.chrom.sizes bigLollyExample2.bb</code></pre> +<pre><code><strong>bedToBigBed</strong> -as=bigLollyExample2.as -type=bed9+1 bigLollyExample2.bed hg38.chrom.sizes bigLollyExample2.bb</code></pre></li> <p> <li> Move the newly created bigBed file (<em>bigLollyExample2.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/bigLollyExample2.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> -<<<<<<< Updated upstream - <pre><code>track type=bigLolly name="bigLolly Example Two" description="A second bigLolly file" bigDataUrl=http://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bigLollyExample2.bb lollyField=pValueLog visibility=full</code></pre></li> - <li> - Go to chr21:15,593,670-15,632,442 to see the data. -======= <pre><code>track type=bigLolly name="bigLolly Example Two" description="A second bigLolly file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigLollyExample2.bb lollyField=pValueLog visibility=full</code></pre></li> ->>>>>>> Stashed changes -</ol> <li> + Go to chr21:15,593,670-15,632,442 to see the data.</li> +</ol> <h3>Example #3</h3> <p> In this example, you will create your own bigBed file to display as a bigLolly from an bed file with the size of the lollipop defined by an extra field, and the height defined by the score field. We'll also turn off the lollipop stems and add some labels and lines on the y axis.</p> <ol> <li> Save <a href="examples/bigLollyExample3.bed">this bed file</a> to your computer.</li> <li> Save the autoSql files <a href="examples/bigLollyExample3.as"><em>bigLollyExample3.as</em></a> - to your computer + to your computer.</li> <li> Download the <code>bedToBigBed</code> <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utility</a>.</li> <li> Save the <a href="hg38.chrom.sizes"><em>hg38.chrom.sizes</em> text file</a> to your computer. This file contains the chrom.sizes for the human hg38 assembly.</li> <li> Use the <code>bedToBigBed</code> utility to create a bigBed file from your sorted BED file, using the <em>bigLollyExample3.bed</em> file and <em>chrom.sizes</em> files created above. </p> <pre><code><strong>bedToBigBed</strong> -as=bigLollyExample3.as -type=bed9+1 bigLollyExample3.bed hg38.chrom.sizes bigLollyExample3.bb</code></pre> -<p> +<p></li> <li> Move the newly created bigBed file (<em>bigLollyExample3.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/bigLollyExample3.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> -<<<<<<< Updated upstream - <pre><code>track type=bigLolly name="bigLolly Example Three" description="A third bigLolly file" bigDataUrl=http://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bigLollyExample3.bb lollySizeField=lollySize visibility=full yAxisLabel.0="0 on 30,30,190 0" yAxisLabel.1="5 on 30,30,190 5" lollyNoStems=on lollyMaxSize=10 yAxisNumLabels=off</code></pre></li> -======= <pre><code>track type=bigLolly name="bigLolly Example Three" description="A third bigLolly file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigLollyExample3.bb lollySizeField=lollySize visibility=full yAxisLabel.0="0 on 30,30,190 0" yAxisLabel.1="5 on 30,30,190 5" lollyNoStems=on</code></pre></li> -</ol> ->>>>>>> Stashed changes <li> - Go to chr21:25,891,755-25,891,870 to see the data. + Go to chr21:25,891,755-25,891,870 to see the data.</li> </ol> <h2>Sharing your data with others</h2> <p> If you would like to share your bigLolly data track with a colleague, learn how to create a URL by looking at Example 6 on <a href="customTrack.html#EXAMPLE6">this page</a>.</p> <h2>Extracting data from the bigLolly format</h2> <p> Because the bigLolly 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>