853914db4ca301e3d1db209c24b9a951dfbb5f4a braney Sun Sep 13 17:24:41 2020 -0700 adding all the bigLolly options to doc diff --git src/hg/htdocs/goldenPath/help/bigLolly.html src/hg/htdocs/goldenPath/help/bigLolly.html index acf8896..6bd047c 100755 --- src/hg/htdocs/goldenPath/help/bigLolly.html +++ src/hg/htdocs/goldenPath/help/bigLolly.html @@ -1,46 +1,45 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser bigLolly Track Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>bigLolly Track Format</h1> <p> -The bigLolly format is a standard bigBed file that generates a lollipop graph. -bigLolly files are compressed and indexed as bigBeds. The trackDb defines the fields used to create -the graph. +The bigLolly format uses a standard bigBed file that is used to generate a lollipop graph. +By default the score is used to decide how high to draw the lollipop, but there are trackDb options to specify which fields to use for the height and width of the lollipop, as well as to draw lines on the graph. <p> -The bigLolly files are in an indexed binary format. The main advantage of this format is that only +The bigBed files used in bigLolly type are in an indexed binary format. The main advantage of this format is that only those portions of the file needed to display a particular region are transferred to the Genome Browser server. The bigLolly file remains on your local web-accessible server (http, https or ftp), not on the UCSC server, and only the portion needed for the currently displayed chromosomal position is locally cached as a "sparse file". If you do not have access to a web-accessible server and need hosting space for your bigLolly files, please see the <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub Help documentation.</p> <a name=bigLolly></a> <h2>bigLolly format definition</h2> <p> -Any bigBed file can be displayed as a bigLolly. +Any bigBed file can be displayed as a bigLolly. See <a href="bigBed.html">bigBed format</a>. <p> <h2>Creating a bigLolly track</h2> <p> -To create a bigLolly track, follow these steps to build a bigBed <a href="goldenPath/help/bigBed.html"> here</a></p> +To create a bigLolly track, follow these steps to build a bigBed <a href="bigBed.html"> here</a></p> <h2>Examples</h2> <h3>Example #1</h3> <p> In this example, you will create a bigLolly custom track using an existing bigBed file, <em>bigBed.bb</em>, located on the UCSC Genome Browser http server. This file contains data for the hg38 assembly.</p> <p> To create a custom track using this bigLolly 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/bigLolly.bb linkDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigLolly.link.bb</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>