586a03e6ff6d676406d62106ae7e2e8539f52a4d dschmelt Tue Feb 4 11:22:26 2020 -0800 Documenting GTF downloads directory #20867 diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index bf0ac78..c1dbeef 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -1,29 +1,30 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser FAQ" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Frequently Asked Questions: Linking to the Genome Browser</h1> <h2>Topics</h2> <ul> <li><a href="#link1">Creating a sharable URL to view specific tracks</a></li> <li><a href="#link2">Linking to the Browser at a specific position</a></li> +<li><a href="zoomVariant">Zooming in or out using a link to ab HGVS identifier</a></li> <li><a href="#trackViz">Setting track visibility via URL</a></li> <li><a href="#custUrl">Loading Custom Tracks with the URL</a></li> <li><a href="#hubUrl">Loading Track Hubs and Assembly Hubs with the URL</a></li> <li><a href="#link3">Linking to gene specific information</a></li> <li><a href="#hgsid">The hgsid parameter</a></li> <li><a href="#moreInfo">Additional URL parameters</a></li> </ul> <a name="link1"></a> <h2>Creating a sharable URL to view specific tracks</h2> <h6>How do I create a link to the Genome Browser to share my data?</h6> <p> The easiest way to save and share tracks from the URL is by <a href="../cgi-bin/hgLogin" TARGET="_blank">logging in</a> to your Genome Browser account and creating a <a href="../goldenPath/help/hgSessionHelp.html">saved session</a>. @@ -48,50 +49,73 @@ This longer format has the flexibility of replacing "hgTracks" with different tool names to share saved settings on the Table Browser (hgTables), Variant Annotation Integrator (hgVai), or Data Integrator (hgIntegrator). This will preserve your option selections and can be useful to share. The following format will bring the recipient to a user's custom Table Browser selections:</p> <p><code>http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&hgS_otherUserSessionName=<sessionName></code></p> <p>Both session link formats have the advantage of being able to add URL parameters to the end. The shorter link format requires a question mark before any URL parameters, with ampersand characters separating different parameters like so: </p> <p><code><a href=http://genome.ucsc.edu/s/view/clinicalzoom?textSize=18>http://genome.ucsc.edu/s/view/clinicalzoom?textSize=18</a></code></p> <p>Both formats require an ampersand between each additional parameter, seen in the longer format like so:</p> <p><code><a href=http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=view&hgS_otherUserSessionName=clinicalzoom&textSize=18>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=view&hgS_otherUserSessionName=clinicalzoom&textSize=18</a></code></p> <a name="link2"></a> <h2>Linking to the Browser at a specific position</h2> -<h6>How do I make a link to a specific genome or position?</h6> +<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> <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 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> + +<a name="zoomVariant"></a> +<h2>Zooming in or out with a link</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><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><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, 24, or 34. Default is a textSize of 8.</li> <li><code><trackName>.heightPer=<###></code> - sets a bigWig track's height to a