Individual sessions may be designated as either shared or non-shared to protect the privacy of confidential data. To avoid having a new shared session from someone else override your existing Genome Browser settings, you are encouraged to open a new web-browser instance or to save existing settings in a session before loading a new shared session.
Note that not all of the Genome Browser mirror sites have all of the session features enabled.
This User's Guide provides a few examples that introduce the features of the Session tool, followed by detailed directions on creating, saving, modifying and sharing sessions.
-You may also wish to reivew two blog posts, +You may also wish to review two blog posts, How to share your UCSC screenthoughts and Sharing Data with Sessions and URLs for more discussions about sessions.
This section contains some example sessions that demonstrate the use of the Session tool. To enable you to view these sessions, we have created a user account with the name Example.
@@ -200,31 +200,31 @@ then be listed by name under My Sessions.Save Settings section.
Type a name into the Save current settings to a local file box. Click the
button to save or display the file. The session will be saved in plain text
(ascii) format by default. To select a compressed format, select one of the options from the
file type returned menu before clicking . If you simply wish to
preview the contents of the file in your browser window, leave the file name blank and click
.Save
Settings section. Click the button to the right of "back up custom
tracks archive .tar.gz". For each genome assembly, the custom track names will be shown along
with individual and total file size. To proceed, click the button. All of the custom track data for the active session will be archived and
compressed. Large custom tracks may take several minutes to finish. To download the archive to
your computer, type in a name for the downloaded archive file and click the button. The file will have a ".tar.gz" extension. Note that Safari
browsers will unzip the archive leaving you with a .tar file in your Downloads directory. Click
the button to return to the Session Management page. To save viewing
settings like track visibilities, highlighting, and sequence positions, use the "Save session
settings to a local file" feature mentioned above.Shared sessions can be opened by other Genome Browser users to whom you've provided one of the following:
Sessions which you've added to the list of Public -Sessions will available to the world. Note that unless you've added them to this list of Public +Sessions will be available to the world. Note that unless you've added them to this list of Public Sessions, your shared sessions will not be available in a general way to other Genome Browser users; they will need at least one of these access methods.
If you choose to keep your session private, other users of the Genome Browser will not be able to access your data or browser configuration. Any confidential data or locations of interest that you are working with will be safe from viewing by others.
The most secure way to control your session is to save the settings to a local file, then deny access to that file by others.
There are five ways to let others know about your saved sessions: @@ -408,47 +408,47 @@ them to load it using the Session tool.
http://genome.ucsc.edu/cgi-bin/hgSession?hgS_doLoadUrl=submit&hgS_loadUrlName=MyUrl
where MyUrl is the URL of your settings file, e.g.,
http://www.mysite.edu/~me/mySession.txt. In this type of link, you may replace
"hgSession" with "hgTracks" to proceed directly to
the Genome Browser.
If you open a shared session while viewing the Genome Browser, it is possible to lose all of your own browser settings. That is, the settings for the newly-opened session will take precedence over your existing settings and will replace them. If you wish to preserve your original settings, you should first save your own settings as a session before opening a new session, or open a new tab or window in your internet browser before loading the new session.
There are four ways to open a shared session, depending on what information you have about the -session. The instructions below assume that you want to replace your current session the new +session. The instructions below assume that you want to replace your current session with the new session. Be sure to preserve your original session first if you don't want to overwrite it.
No other user can delete your saved sessions, even if you have provided access to your sessions to them. Other users simply have a copy of your session.
Unlike most other browser preferences, the session settings are not saved in your Genome Browser "cart". Therefore, if you choose to reset the Genome Browser, it will not delete your saved sessions.
-Your saved sessions will not be expired and will available you (and others if you +Your saved sessions will not be expired and will be available to you (and others if you share them) until you delete them. We have discontinued our previous policy of removing saved sessions and associated custom track data after four months. However, note that the UCSC Genome Browser is not a data storage service; please keep a local backup of your session contents and custom track data.
The Session Gallery is a collection of track views that help highlight viewing different topics in the browser. The sessions in the Session Gallery were created in the browser and then saved to a local file, which was then uploaded to an online location. This allows creating a single link, such as http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=U, where U is the URL of the session file, e.g., http://www.mysite.edu/~me/mySession.txt, @@ -596,59 +596,59 @@ to: BAM, bigBed, WIG, bigWig, and VCF data types. The last attribute, bigDataUrl, is required for remotely hosted data types such as BAM, CRAM, bigBed, bigWig, and VCF.
Adding more attribute=value pairs can further customize the display. Here is a custom track that uses the visibility and -description atrributes: +description attributes:
track type=bam visibility=dense name="My BAM" description="Example from the ENCODE RNA-seq CSHL track" bigDataUrl=http://hgdownload.gi.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqA549CellPapAlnRep1.bamThere are also options to configure the display of your BAM files, such as a density plot feature that will dynamically process the underlying BAM into a wiggle signal.
A bigWig file is useful when trying to display dense, continuous data. Read more on the bigWig track format help page. Here is an example bigWig track that is colored red, instead of the default black color, that can be pasted directly into the Custom Tracks Page:
track color=255,0,0 name="HeLa-S3 nucleus minus signal" description="RNA Subcellular CAGE Localization from ENCODE/RIKEN" type=bigWig visibility=full bigDataUrl=http://hgdownload.gi.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHelas3NucleusPapMinusSignalRep1.bigWigThere are also options to configure the display of your wiggle tracks, such as changing the track height or type of graph.
After creating your custom tracks and viewing your data on the Genome Browser, you can save all of your tracks and settings to a snapshot of the Genome Browser called a session. You can - easily save a session by following these five steps:
+ easily save a session by following these steps: