5bee5ceb3d7e48e64c5c6b1839b9a0100b5e5e2d brianlee Fri Jun 10 06:40:41 2022 -0700 Adding some anchors to FAQlink.html, no RM diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index e38adc4..5eec344 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -100,92 +100,92 @@ <code id="hgS_loadUrlName">hgS_loadUrlName=<URL></code> allowing you to externally maintain your session, or update it as you wish. Here is an example:</p> <p><code><a href="https://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.stopCodons"> https://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.stopCodons</a></code></p> <a name="link2"></a> <h2>Linking to the Browser at a specific position, or default position</h2> <h6>How do I make a link to a specific genome, position, or HGVS variant?</h6> <p> You can link to a specific genome assembly and position in the Genome Browser using a URL with the <code>db=</code> and <code>position=</code> parameters.</p> <p><code>http://genome.ucsc.edu/cgi-bin/hgTracks?db=<assembly>&position=<position></code></p> <p> Where:</p> <ul> - <li> + <li id="db"> <code>db</code> - designates a specific genome assembly. For example, <code>db=hg19</code> refers to the Feb. 2009 human genome release. For a list of db parameter values that correspond to UCSC assemblies, see the <a href="FAQreleases.html#release1">list of UCSC releases</a>.</li> - <li><code>position</code> - can be any search term for the genome specified, including + <li id="position"><code>position</code> - can be any search term for the genome specified, including a position range or a gene identifier. This often takes the form of <code>position=chr1:35000-40000</code>.</li> </ul> <p>The following link is an example of a URL that declares assembly and position:</p> <p><code><a href="../cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000</a></code></p> <h6>How do I make a link to the default position of a genome?</h6> <p> You can link directly to the default position of an assembly by passing the <code>position=default</code> parameter. This can be helpful in cases where a track exists on multiple assemblies, and you want to build links to each of them. If no position variable is passed, the Genome Browser assumes the default position for the default assembly (hg38).</p> <p> Here is an example which opens the uniprot track at the default position for sacCer3:</p> <p><code><a href="/cgi-bin/hgTrackUi?db=sacCer3&g=uniprot&position=default">http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=sacCer3&g=uniprot&position=default</a></code></p> <a name="zoomVariant"></a> <h2>Zooming in or out with a link — HGVS </h2> <h6>How do I zoom out using a link to a HGVS identifier?</h6> <p> To link to a specific HGVS identifier, you can construct a link with the HGVS identifier in the position field instead of coordinates. The default padding is 5bp on either side, but you can always zoom in or out with <code>hgt.out1=submit</code> or <code>hgt.in1=submit</code>. The numbers 1 through 4 zoom in or out corresponding to the buttons above the track window. The following lists the zoom levels of each number, applicable to zooming in or out:</p> <ul> -<li><code>hgt.out1=submit</code> zooms out 1.5x</li> -<li><code>hgt.out2=submit</code> zooms out 3x</li> -<li><code>hgt.out3=submit</code> zooms out 10x</li> -<li><code>hgt.out4=submit</code> zooms out 100x</li> +<li id="hgt.out1"><code>hgt.out1=submit</code> zooms out 1.5x</li> +<li id="hgt.out2"><code>hgt.out2=submit</code> zooms out 3x</li> +<li id="hgt.out3"><code>hgt.out3=submit</code> zooms out 10x</li> +<li id="hgt.out4"><code>hgt.out4=submit</code> zooms out 100x</li> </ul> <p> The following link is an example which leads to the variant NM_00257:c.1208G>T and zooms out 3x:</p> <p> <code><a href="../cgi-bin/hgTracks?db=hg19&position=NM_000257:c.1208G%3ET&hgt.out2=submit">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=NM_000257:c.1208G>T&hgt.out2=submit</a></code></p> <a name="trackViz"></a> <h2>Setting Track Visibility via URL</h2> <h6>How do I create a custom URL to control the visibility of specific tracks?</h6> <p> You can control the visibility of tracks from the URL with the following parameters, each linked by the "&" sign, similar to position parameters. For more information, please see the <a href="../goldenPath/help/customTrack.html#optParams" target ="_blank">optional URL parameters</a> section of the Custom Tracks User's Guide.</p> <ul> -<li><code>hideTracks=1</code> - hides all tracks</li> +<li id="hideTracks"><code>hideTracks=1</code> - hides all tracks</li> <li><code><trackName>=hide|dense|pack|full</code> - sets specified track or subtrack to a chosen visibility</li> -<li><code>textSize=<number></code> - sets browser text size to either 6, 8, 10, 12, 14, 18, +<li id="textSize"><code>textSize=<number></code> - sets browser text size to either 6, 8, 10, 12, 14, 18, 24, or 34. Default is a textSize of 12.</li> <li><code><trackName>.heightPer=<###></code> - sets a bigWig track's height to a particular number of pixels (between 20-100)</li> -<li><code>ignoreCookie=1</code> - removes pre-existing user settings like track selection, custom +<li id="ignoreCookie"><code>ignoreCookie=1</code> - removes pre-existing user settings like track selection, custom tracks, and track hubs</li> </ul> <p> For example, you can use the following command to hide every track (hideTracks=1), set the genome database to hg38 (db=hg38), set the mappability track to full visibility (mappability=full), and set the umap track height to 100 pixels (umap24Quantitative.heightPer=100). Each of these parameters can be used individually or in combination.</p> <p><code><a href="../cgi-bin/hgTracks?db=hg38&ignoreCookie=1&hideTracks=1&mappability=full&umap24Quantitative.heightPer=100"> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&mappability=full&umap24Quantitative.heightPer=100</a></code></p> <p>Composite tracks have additional URL parameters that encode options to hide, select, and display subtracks.</p> <ul> <li><code><trackName>_hideKids=1</code> - hides a specific composite track's subtracks</li>