Questions and feedback on this User's Guide are welcome.
User questions and answers on Sessions and other topics are available in the Genome Browser mailing list.
The Session tool allows you to configure your browser with specific track combinations, including custom tracks, and save the configuration options. Multiple sessions may be saved for future reference, for comparing different data sets, or for sharing with your colleagues. Saved sessions will not be expired, however, we still recommend that you keep local back-ups of your session contents and any associated custom tracks. BLAT result tracks persist for at least 48 hours after the last time they are viewed. The creation date of a session can be viewed in the Session Management menu. This date only reflects the initial creation of the Session and is not updated when sessions are edited. Descriptive text can also be added to a session in the Session Details menu.
This feature may be accessed via the Session link in the top blue navigation bar in any assembly. To ensure privacy and security, you must create an account and log in before using the session manager.
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.
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.
This example shows the primate (chimp and rhesus) nets for chromosome 2 in the hg17 human assembly
— the primate chromosome that fused in humans. We first configured our browser view with the
desired settings, and then saved the session so that we could share it. We named our session
hg17_chr2_primate.
There are several ways for you to view this session:
Session Management section under the
Load Settings heading, enter this information:
user: Example
session name: hg17_chr2_primate
Click the button next to the session name box to load the session. To view
the session in the Genome Browser, click the Genome Browser link in the top blue
navigation bar.
Here is a UCSC browser session I'd like to share with you:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Examples&hgS_otherUserSessionName=hg17_chr2_primate. By clicking this link, you can open the session in your browser.
Session
Management section under the Load Settings header, enter the URL where this file
is located:
http://genome.ucsc.edu/goldenPath/help/examples/session_example1.txtUpdated Session
section.This example shows the Human Accelerated Region (HAR1) in the hg18 assembly. Eighteen differences exist in a region of 118 bases between human and all other mammals extending back to the chicken. The two sessions in this example show the same browser position at two levels of detail: Example 2a is zoomed out; Example 2b is zoomed in.
To view these sessions in your browser, you can use any of the methods described in Example 1:
user: Example
session name: hg18_HAR1user: Example
session name: hg18_HAR1_zoom http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&
hgS_otherUserName=Example&hgS_otherUserSessionName=hg18_HAR1http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&
hgS_otherUserName=Example&hgS_otherUserSessionName=hg18_HAR1_zoom.http://genome.ucsc.edu/goldenPath/help/examples/session_example2a.txthttp://genome.ucsc.edu/goldenPath/help/examples/session_example2b.txtIt is easy to create a session to save or share. Simply configure the Genome Browser as you wish, then navigate to the Session tool by clicking on the My Data pulldown in the top blue navigation bar. Follow these steps to save your session:
Save Settings section of
the page. Type a name into the Save current settings as named session box. Choose
whether or not you would like to share your sessions with others. If the
allow this session to be loaded by others box is checked, anyone will be able to view
your Genome Browser settings (including your custom tracks) if you provide them with your user and
session name. Note that your session is not automatically available to the general public
if you choose this option: you must provide the user and session name to other individuals for
them to view it. This helps to ensure the confidentiality of your private data. After naming the
session and choosing your sharing option, click the button. Your session will
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 "backup 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.cd Downloads
mkdir someproject
cd someproject
tar -xzf ../someproject.tar.gztar -xf ../someproject.tarcd hg38
cat *.ct > hg38_all.ctgzip hg38_all.ct
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When you save a session, it is added to the My Sessions list on the Session page. Each session entry is listed by name and offers the following options to open, share, and manipulate it:
Each session has an associated details page that you can click into from the Session Management menu. The Session Details menu allows you to edit the Session Name, to add descriptive text and to change whether or not the session is shared with others. Like the Session Management menu, if you click "use" that session will be loaded as the current session and if you click "delete" the session will be deleted. The "Created on" date reflects the date that the session was originally created and will not be updated to reflect any edits.
When you create a session using the Session tool, you may designate it as either shared or non-shared. By default, new sessions are created as shared and must be explicitly changed to non-shared status.
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, 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:
Browser hyperlink. Additionally, each session entry in the
My Sessions list has a Browser hyperlink. Click either Browser
link to open the Genome Browser with the session loaded. You can obtain the URL of the Genome
Browser page by capturing the Browser hyperlink via right-click before you proceed
to the Browser graphical view. You can then store the URL, create a bookmark or share the link
with others.
The UCSC site and supported mirrors display short session links similar to the following:
http://genome.ucsc.edu/s/YourUserName/YourSessionName
Previously, longer links were used:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=YourUserName&hgS_otherUserSessionName=YourSessionName
System administrators of mirrors can introduce Apache redirects from the shorter links
that will redirect to the longer links and enable the links to display for new sessions by
setting hgSession.shortLink=on in the mirror's configuration files. Both links
can be modified to include URL parameters, such as
position=chr10:69,644,222-69,644,999 in these examples:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=view&hgS_otherUserSessionName=clinicalzoom&position=chr10:69,644,222-69,644,999
http://genome.ucsc.edu/s/view/clinicalzoom?position=chr10:69,644,222-69,644,999
Email link. Click this link to automatically invoke your email tool with a
message containing the Genome Browser URL, which you can then send to others.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. Be sure to preserve your original session first if you don't want to overwrite it.
Use settings from a URL box, then click to display the Genome
Browser using the new session settings.
It's easy to make changes to an existing session. Reconfigure the Genome Browser as you wish, then resave the session with the same name. The Session tool will warn you that you are about to overwrite an existing session.
You can also edit any descriptive text associated with your session as well as whether or not the session can be shared in the Session Details menu. Note that editing a session will not alter the creation date listed in the Session Management menu.
If you previously shared this session with others, they will not see the changes until they reload your newly-edited session.
In addition to displaying standard UCSC tracks in your session, you can also display the following user-generated tracks:
Before you create and save your session, be sure to upload your Custom Track or Genome Graph track. These user-generated tracks associated with a saved session will not expire. BLAT results always have a lifespan of 48 hours, even if they are part of a session. However, if you generate a custom track from your BLAT results, they will be saved in your session.
In the Session Management section under My Sessions, press the button next to the session name you would like to delete. This will permanently delete all details of the session from the UCSC server. Any saved links to that session will no longer work.
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 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, enabling users to maintain external control of the content file for easy update.
The Nucleic Acids Research (NAR) journal now requires manuscript submissions to contain a private Session link to your data in the UCSC Genome Browser that allows reviewers to access data. These instructions will show you how to upload, view, and share your data.
You can view your own private data by uploading your annotation files to the Genome Browser as custom tracks; visit our custom track help page to learn more. To summarize the steps to upload your data, you will need to:
Creating the track line may be the most challenging step since many configuration options exist. The track line begins with the track keyword, followed by one or more attribute=value pairs where the order of the attributes does not matter. Here are some examples:
The simplest example of a BAM custom track is the following track line:
track name="My BAM" type=bam bigDataUrl=http://www.mysite.edu/~me/my_sorted.bamIn the example above, the name attribute defines the name of your custom track. The second attribute, type, is required for some data types, but not limited 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:
track type=bam visibility=dense name="My BAM" description="Example from the ENCODE RNA-seq CSHL track" bigDataUrl=http://hgdownload.soe.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.soe.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:
After saving your session, you will now be able to share your session link with others. There are three different ways that you can share your session:
You can edit URLs to directly go to different parts of the Genome Browser such as by changing hgSession to hgTracks, e.g.,
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.relaHaving hgTracks in the session URL will take the viewer to the main page of the Genome Browser instead of the sessions page.
Creating a track hub allows you to group and organize your annotation tracks, but is limited to compressed binary indexed formats that can be remotely hosted. This will require the use of a web-accessible location to load the track hub in the UCSC Genome Browser. If your institution does not provide web space for you, you can look into hosting your binary files at a couple different web hosting services, such as CyVerse or figshare. If you would like to learn more about using track hubs, please read our Track Hub help page.
If you have any questions regarding the creation of your custom track or session, please feel free to contact us. Before submitting a question, we strongly encourage you to search our mailing list archives, our website, and our wiki for the answer. [an error occurred while processing this directive]