da9bfb0be4cf7ad610abb4f1e8d082b286ec759b dschmelt Fri May 3 16:19:25 2019 -0700 Fixed typos #21313 diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index 7f4bfaa..0943684 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -20,56 +20,56 @@

Creating a sharable URL to view specific tracks

How do I create a link to the Genome Browser to share my data?

The easiest way to save and share tracks from the URL is by logging in to your Genome Browser account and creating a saved session. Saved sessions are a versatile way to share data that may include native data, Custom Tracks, and Track Hubs.

You will be able to save and share Genome Browser sessions with the following format:

http://genome.ucsc.edu/s/userName/sessionName

-Or if you prefer the a modifiable, longer URL; use this format:

+Or if you prefer a modifiable, longer URL; use this format:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=[UserName]&hgS_otherUserSessionName=[SessionName]

For instructions on creating a saved session, go to the Saved Session Help page.

If you want to specify track settings in a URL directly, please read the section on changing track visibility via URL for a complete description. Note that these URL parameters do not work with the shorter session URLs.

Linking to the Browser at a specific position

How do I make a link to a specific genome or position?

You can link to a specific genome assembly and position in the Genome Browser using a URL with the db= and position= parameters:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=[db]&position=[position]

Where:

db - designates a specific genome assembly. For example, db=hg19 refers to the Feb. 2009 human genome release. For a list of db parameter values that correspond to UCSC assemblies, see the list of UCSC releases.
position - can be any seach term for the genome specified, including +
position - can be any search term for the genome specified, including a position range or a gene identifier. This often takes the form of position=chr1:35000-40000.

The following link is an example of a URL that declares assembly and position:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000

The hgsid parameter

What is the hgsid parameter and should I include it in Genome Browser links?

The hgsid is a temporary user ID that stores setting and custom track information in the URL. Including it in any shared URLs is a privacy concern, and it should be removed when constructing any links to the Genome Browser. Creating Saved Sessions is the recommended way to share Genome Browser information.

@@ -79,31 +79,31 @@

Setting Track Visibitlies via URL

How do I create a custom URL to control the visibility of specific tracks?

You can control the visibility of tracks from the URL with the following parameters, each linked by the "&" sign, similar to position commands. For the full list, please see the optional URL parameters section of the Custom Tracks User's Guide. Note that italic text indicates a user choice, not a working example.

hideTracks=1
trackName=hide|dense|pack|full
textSize=number

For example, you can use the following command to hide every track and set the knownGene track to -the pack visibiblity:

+the pack visibility:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack

Composite tracks have additional URL parameters that encode options to hide, select, and display subtracks.

trackName_hideKids=1
trackName_sel=1
ignoreCookie=1

For example, the following URL hides all tracks (&hideTracks=1), hides a specific composite track's default subtracks (&refSeqComposite_hideKids=1), turns on one specific subtrack (&ncbiRefSeqCurated=full), and checks a box to display that subtrack (&ncbiRefSeqCurated_sel=1).

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&refSeqComposite_hideKids=1&ncbiRefSeqCurated=full&ncbiRefSeqCurated_sel=1