aad219b68b73b72b0e1ef012d91081b21f42158f kuhn Thu Sep 9 15:24:39 2021 -0700 moved query bozes above the fold to be more obvious diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index 09ed9e7..d3dcf6c 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -1,76 +1,86 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser User's Guide" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="$ROOT/redmineWidget.html" --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Genome Browser User Guide</h1> <h2>Contents</h2> +<div class="row"> +<div class="col-md-4"> + + <h6><a href="#What">What does the Genome Browser do?</a></h6> <h6><a href="#FineTuning">Configuring the Genome Browser display</a></h6> <h6><a href="#IndivTracks">Annotation track descriptions</a></h6> <h6><a href="#BLATAlign">Using BLAT alignments</a></h6> <h6>Getting Started with:</h6> <ul> <li> <h6><a href="#GetStarted">Genome Browser Gateway</a></h6> <li> <h6><a href="#TableBrowser">Table Browser</a></h6> <li> <h6><a href="#Sessions">Using Sessions</a></h6> <li> <h6><a href="hgGeneGraph.html">Gene and Pathway Viewer</a></h6> <li> <h6><a href="#GenomeGraphs">Genome Graphs</a></h6> </ul> <h6><a href="#TrackFormatDNA">DNA text formatting</a></h6> <h6><a href="#Convert">Converting data between assemblies</a></h6> <h6><a href="#Download">Downloading genome data</a></h6> <h6><a href="#CustomTracks">Creating and managing custom annotation tracks</a></h6> <h6><a href="#TrackHubs">Getting started on Track Hubs</a></h6> <h6><a href="#UseOneFile">Track Hubs in a single file</a></h6> <h6><a href="#VisiGeneHelp">Using the VisiGene Image Browser</a></h6> -<hr> + +</div> +<div class="col-md-8"> + <form name="googleForm1" method="get" action="http://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+' site:genome.ucsc.edu/goldenPath/help';"> <p> Search the Genome Browser help pages: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=30 maxlength=255 value=""> <input type="submit" value="Submit"> </p> </form> <form name="googleForm2" method="GET" action="http://www.google.com/search" onSubmit="document.googleForm2.q.value=document.googleForm2.qq.value+' site:genome.ucsc.edu/';"> <p> Search the entire Genome Browser website: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=30 maxlength=255 value=""> <input type="submit" value="Submit"> </p> </form> <p> <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">Browse</a> the Genome Browser mailing list.</p> <p> <a href="../../contacts.html">Questions and feedback are welcome</a>.</p> + </div> +</div> + <!-- =======What does the Genome Browser do?======= --> <a name="What"></a> <h2>What does the Genome Browser do?</h2> <p> As vertebrate genome sequences near completion and research re-focuses on their analysis, the issue of effective sequence display becomes critical: it is not helpful to have 3 billion letters of genomic DNA shown as plain text! As an alternative, the UCSC Genome Browser provides a rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more). Half of the annotation tracks are computed at UCSC from publicly available sequence data. The remaining tracks are provided by collaborators worldwide. Users can also add their own custom tracks to the browser for educational or research purposes.</p> <p> The Genome Browser stacks annotation tracks beneath genome coordinate positions, allowing rapid