3a1dad7107c1eced5debd13372747f42853c4211 kuhn Thu Sep 9 16:28:26 2021 -0700 added a couple of landmarks to make it easier to get around in file diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index d3dcf6c..25b65be 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -739,30 +739,31 @@ <p> To print or save the image to a file: <ol> <li> In the blue navigation bar at the top of the screen, from the "View" menu, click the "PDF/PS" link.</li> <li> Click one of the PDF or EPS links.</li> </ol> <p> NOTE: If you have configured your browser image to use one of the larger font sizes, the text in the resulting screen shot may not display correctly. If you encounter this problem, reduce the Genome Browser font size using the <a href="#TRACK_CONFIG">Configuration utility</a>, then repeat the save/print process.</p> +<!-- =======BLAT======= --> <a name="BLATAlign"></a> <h2>Using BLAT alignments</h2> <p> BLAT (BLAST-Like Alignment Tool) is a very fast sequence alignment tool similar to BLAST. For more information on BLAT's internal scoring schemes and its overall n-mer alignment seed strategy, refer to W. James Kent (2002) <a href="http://www.genome.org/cgi/content/abstract/12/4/656" target="_blank">BLAT - The BLAST-Like Alignment Tool</a>, <em>Genome Res</em> 12:4 656-664.</p> <p> On DNA queries, BLAT is designed to quickly find sequences with 95% or greater similarity of length 25 bases or more. It may miss genomic alignments that are more divergent or shorter than these minimums, although it will find perfect sequence matches of 32 bases and sometimes as few as 22 bases. The tool is capable of aligning sequences that contain large introns. On protein queries, BLAT rapidly locates genomic sequences with 80% or greater similarity of length 20 amino acids or more. In general, gene family members that arose within the last 350 million years can generally be detected. More divergent sequences can be aligned to the human genome by using NCBI's BLAST and @@ -1382,30 +1383,31 @@ <li><strong>.sql file:</strong> the SQL commands used to create the table.</li> <li> <strong>.txt.gz file:</strong> the MariaDB database table data in tab-delimited format and compressed with gzip.</li> </ul> <p> Schema descriptions for all tables in the genome annotation database may be viewed by using the "describe table schema" button in the <a href="#TableBrowser">Table Browser</a>.</p> <p> <em>Cross-species alignments</em> directories, such as the <em>vsMm4</em> and <em>humorMm3Rn3</em> directories in the hg16 assembly, contain pairwise and multiple species alignments and filtered alignment files used to produce cross-species annotations. For more information, refer to the READMEs in these directories and the description of the <a href "../../FAQformat.html#format5">Multiple Alignment Format</a> (MAF).</p> +<!-- =======Custom tracks======= --> <a name="CustomTracks"></a> <h2>Creating custom annotation tracks</h2> <!--#include virtual="customTrackText.html"--> <a name="TrackHubs"></a> <h2>Getting started on Track Hubs</h2> <p> Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser alongside native annotation tracks. Hubs are a useful tool for visualizing a large number of genome-wide data sets. The <a href="../../cgi-bin/hgHubConnect" target="_blank">Track Hub</a> utility allows efficient access to data sets from around the world through the familiar Genome Browser interface. Browser users can display tracks from any public track hub that has been registered with UCSC. Additionally, users can import data from unlisted hubs or can set up, display, and share their own track hubs.</p> <p>