69d2a32c5a3d72b28818c7ef59affd601ce25522 kuhn Fri Jun 5 19:00:14 2020 -0700 standardized nominclature to key=<value> in #SHARE section. removed some whitespace diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index 7ca861a..d5da05f 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -668,99 +668,99 @@ <h2>Sharing your annotation track with others</h2> <p> To make your Genome Browser annotation track viewable by people on other machines or at other sites, follow the steps below.</p> <p> <strong>Step 1.</strong> Put your formatted annotation file on your web site. Be sure that the file permissions allow it to be read by others.</p> <p> <strong>Step 2.</strong> Construct a URL that will link this annotation file to the Genome Browser. The URL must contain 3 pieces of information specific to your annotation data:</p> <ul> <li> The species or genome assembly on which your annotation data is based. To automatically display the most recent assembly for a given organism, set the <em>org</em> parameter: <em>e.g.</em> <code>org=human</code>. To specify a particular genome assembly for an organism, use the - <em>db</em> parameter, <code>db=database_name</code>, where <em>database_name</em> is the UCSC + <em>db</em> parameter, <code>db=<databaseName></code>, where <em>databaseName</em> is the UCSC code for the genome assembly. For a list of these codes, see the Genome Browser <a href="/FAQ/FAQreleases.html#release1" target="_blank">FAQ</a>. Examples of this include: - db=hg16 (Human July 2003 assembly), db=mm6 (Mouse Mar. 2005 assembly).</li> + db=hg38 (Human Dec. 2013 assembly = GRCh38), db=mm10 (Mouse Dec. 2011 assembly = GRCm38).</li> <li>Additionally, particular genome assemblies, including assemblies in assembly hubs, can be specified using - the <em>genome</em> parameter, <code>genome=database_name</code>, which acts in the same manner as + the <em>genome</em> parameter, <code>genome=<databaseName></code>, which acts in the same manner as the <em>db</em> parameter. Here is an example using the house mouse (<i>Mus musculus</i>, 129S1_SvImJ) assembly hub: <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt</a></li> <li> The genome position to which the Genome Browser should initially open. This information is of the - form <code>position=chr_position</code>, where <em>chr_position</em> is a chromosome number, with + form <code>position=<chrPosition></code>, where <em>chrPosition</em> is a chromosome number, with or without a set of coordinates. Examples of this include: position=chr22, position=chr22:15916196-31832390.</li> <li> The URL of the annotation file on your web site. This information is of the form - <code>hgt.customText=URL</code>, where <em>URL</em> points to the annotation file on your website. + <code>hgt.customText=<url></code>, where <em>url</em> points to the annotation file on your website. An example of an annotation file URL is <a href="test.bed" target="_blank">http://genome.ucsc.edu/goldenPath/help/test.bed</a>.</li> </ul> <a name="optParams"></a> <p> You can add other optional parameters to the URL: (Note: Display may vary if you have conflicting cart variables, for example having both hide all and highlight features.) <ul> <li> <code>guidelines=on/off</code> - activate or deactivate the blue guidelines - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&guidelines=off" target="_blank">example link</a> to switch off blue guidelines</li> <li> - <code>hgFind.matches=listOfNames</code> - highlight features given their names - + <code>hgFind.matches=<listOfNames></code> - highlight features given their names - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgFind.matches=uc010naf.1,uc011mcz.1" target="_blank">example link</a> to highlight two transcripts of the ABO gene</li> <li> <code>hgt.reset=1</code> - show only the default tracks - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.reset=1" target="_blank" >example link</a></li> <li> <code>hgt.toggleRevCmplDisp=1</code> - show the reverse-complement - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.toggleRevCmplDisp=1" target="_blank">example link</a> to show the reverse-complement of the ABO gene</li> <li> <code>hgt.labelWidth=<number></code> - set the size of the left-side label area - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.labelWidth=50" target="_blank">example link</a> to increase the label area to 50 characters</li> <li> <code>hideTracks=1</code> - hide all tracks - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hideTracks=1" target="_blank">example link</a> to show no tracks at all</li> <li> <code>hideTracks=1&<trackName>=full|dense|pack|hide</code> - hide all tracks and show other tracks - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hideTracks=1&cytoBand=pack" target="_blank">example link</a> to show only the Chromosome Bands track and nothing else</li> <li> - <code>highlight=<DB>.<CHROM>:<START>-<END>#<COLOR>|...</code> - + <code>highlight=<db>.<chrom>:<chromStart>-<chromEnd>#<color>|...</code> - highlight one or more regions in a given color on the image. Note that the arguments have to be URL-encoded for Internet browsers, so ":" becomes "%3A", "#" becomes "%23" and "|" becomes "%7"C. - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136136597-136139844&highlight=hg19.chr9%3A136138630-136139650%23AA0000%7Chg19.chr9%3A136136630-136137650%230000FF" target="_blank">example link</a> to highlight two parts of the ABO locus in red and blue.</li> <li> <code>ignoreCookie=1</code> - uses default user settings like track selections, custom tracks, and track hubs - <a href="../../cgi-bin/hgTracks?db=hg19&ignoreCookie=1" target="_blank">example link</a> to show the default tracks and positions for hg19</li> <li> - <code>oligoMatch=pack&hgt.oligoMatch=DNASEQ</code> - switch on the Short Match track and + <code>oligoMatch=pack&hgt.oligoMatch=<dnaSeq></code> - switch on the Short Match track and highlight a matching sequence - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&oligoMatch=pack&hgt.oligoMatch=TATAWAR" target="_blank">example link</a> to highlight the TATAWAR motif in the ABO locus</li> <li> <code>pix=<number></code> - set the width of the image in pixels - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&pix=300" target="_blank">example link</a> to create a 300-pixel wide image</li> <li> <code>textSize=<number></code> - set the size of text font - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&textSize=12" target="_blank">example link</a> to increase the text font size to 12 pixels</li> <li> <code><trackName>=full|dense|pack|hide</code> - show the default tracks adding a track and set it to full, dense, pack or hide visibility - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&cytoBand=pack" @@ -791,31 +791,31 @@ protocol), this information can be included in the URL using the format protocol://user:password@server.com/somepath. Only Basic Authentication is supported for HTTP. Note that passwords included in URLs are not protected. If a password contains a non-alphanumeric character, such as $, the character must be replaced by the hexadecimal representation for that character. For example, in the password mypwd$wk, the $ character should be replaced by %24, resulting in the modified password mypwd%24wk.</p> <p> For integration into your own website e.g. in an html IFRAME, you can obtain the track image only, without the rest of the genome browser user interface, by replacing hgTracks in the URL with hgRenderTracks, like in this example:</p> <pre><code><a href="http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630" target="_blank">http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630</a></code></pre> <p> Combine the above pieces of information into a URL of the following format (the information specific to your annotation file is highlighted):</p> -<pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?org=<font color="000099"><em>organism_name</em></font>&position=<font color="000099"><em>chr_position</em></font>&hgt.customText=<font color="000099"><em>URL</em></font></code></pre> +<pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?org=<font color="000099"><em><organismName></em></font>&position=<font color="000099"><em><chrPosition></em></font>&hgt.customText=<font color="000099"><em><url></em></font></code></pre> <p> <strong><em>Example #5:</em></strong><br> The following URL will open up the Genome Browser window to display chr22 of the latest human genome assembly and will show the annotation track pointed to by the URL http://genome.ucsc.edu/goldenPath/help/test.bed: <pre><code <a class="insideLink" href="../../cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed</a></code></pre> <p> <strong>Step 3.</strong> Provide the URL to others. To upload a custom annotation track from a URL into the Genome Browser, paste the URL into the large text edit box on the Add Custom Tracks page, then click the Submit button.</p> <p> If you'd like to share your annotation track with a broader audience, send the URL for your track—along with a description of the format, methods, and data used—to the UCSC Genome