bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigLolly.html src/hg/htdocs/goldenPath/help/bigLolly.html index 633585b2d57..399899a6652 100755 --- src/hg/htdocs/goldenPath/help/bigLolly.html +++ src/hg/htdocs/goldenPath/help/bigLolly.html @@ -93,31 +93,31 @@ <li> Go to chr21:17,030,007-17,055,589 to see the data.</li> </ol> <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> to your computer.</li> <li> Download the <code>bedToBigBed</code> - <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utility</a>.</li> + <a href="http://hgdownload.gi.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></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> <pre><code>track type=bigLolly name="bigLolly Example Two: SNP data" description="A second bigLolly file" bigDataUrl=http://genome.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.</li> </ol> @@ -125,31 +125,31 @@ <p> In this example, you will create your own bigBed file to display as a bigLolly from a bed file with the size of the lollipop defined by an extra field (<code>lollySizeField=lollySize</code>) where the numbers in this field are similar to a radius and define circle size. To avoid large circles from being clipped, the setting <code>lollyMaxSize=10</code> ensures circles of size 10 fully display. Also, to turn off the lollipop stems, the setting <code>lollyNoStems=on</code> is added. Finally, the settings <code>yAxisLabel.0="0 on 30,30,190 0"</code> and <code>yAxisLabel.1="5 on 30,30,190 5"</code> adds labels and lines on the y axis where 30,30,190 defines the color.</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.</li> <li> Download the <code>bedToBigBed</code> - <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utility</a>.</li> + <a href="http://hgdownload.gi.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></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> <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" lollyMaxSize=10 lollyNoStems=on</code></pre></li> <li> Go to chr21:25,891,755-25,891,870 to see the data.</li> </ol> @@ -165,38 +165,38 @@ <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 from <a href="#example1">Example 1</a> 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</code></pre> <p> If you would like to share your bigLolly 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> on the custom track help page.</p> <a name=extracting_data></a> <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> +<a href="http://hgdownload.gi.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> <a name=troubleshooting></a> <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 the end of the chromosome. If these are present, run the <code>bedClip</code> program -(<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">available here</a>) to remove the problematic +(<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">available here</a>) to remove the problematic row(s) in your input file before running the <code>bedToBigBed</code> program.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->