Sessions User's Guide

Contents

Introduction

Some simple examples

Creating a session

Creating a session — video demonstration

Session details

Sharing a session

Editing an existing session

Displaying your own tracks in a session

Deleting a session

Lifespan of a session

Session gallery

Help for Nucleic Acids Research submitters

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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.

Introduction

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.

You may also wish to reivew two blog posts, How to share your UCSC screenthoughts and Sharing Data with Sessions and URLs for more discussions about sessions.

Some simple examples

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.

Example 1

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:

• Manually load and open the session. Open the Session tool. In the Session Management section under the Load Settings heading, enter this information:

  user: Example
  session name: hg17_chr2_primate 

  Click the submit 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.

• Open a session link sent by email. After we created and saved this session, we could have clicked the Email link to automatically send a message to one or more recipients with the following contents and clickable link:

  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.

• Open a session from a local file. Alternatively, if we had saved the browser settings to a local file, we could have simply provided the location of that file for you to load into your browser to view our session. Click here to see such a settings file. This method works best when the file is in a location that you can access from your own computer or network. For this example, you can copy this file and paste it into a file on your own machine, then load it into the Session tool.
• Open a session from a URL. Because you do not have access to our file system where this session file resides, it will be easier for you to load it using a URL. To do this, open the Session tool. In the 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.txt

  
  Then, click the submit button to load the session settings. To view the session in the Genome Browser, press the Browser link in the Updated Session section.

Example 2

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:

• Manually load and open the session.
  Example 2a:

  user: Example
  session name: hg18_HAR1

  Example 2b:

  user: Example
  session name: hg18_HAR1_zoom 

• Open a session link sent by email.
  Example 2a:

  http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&
  hgS_otherUserName=Example&hgS_otherUserSessionName=hg18_HAR1

  Example 2b:

  http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&
  hgS_otherUserName=Example&hgS_otherUserSessionName=hg18_HAR1_zoom.

• Open a session from a local file.
  Example 2a: Copy the contents of this file to a file on your own machine, then load it into the Session tool.
  Example 2b: Copy the contents of this file to a file on your own machine, then load it into the Session tool.


• Open a session from a URL.
  Example 2a: Paste this URL into the Session tool:

  http://genome.ucsc.edu/goldenPath/help/examples/session_example2a.txt

  Example 2b: Paste this URL into the Session tool:

  http://genome.ucsc.edu/goldenPath/help/examples/session_example2b.txt

Creating a session

It 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:

• Log in to the Genome Browser. To ensure privacy and security, you must create an account and/or log in to use the Session tool. You will not have to repeat the login step unless you sign off from the Session tool or close your Genome Browser.
• Create a named session. Scroll down to the 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 submit button. Your session will then be listed by name under My Sessions.
• Save session settings to a file. Alternatively, you can create a file from your session settings that can be saved to your local machine or posted to a URL for access or sharing. To do this, go to the Save Settings section. Type a name into the Save current settings to a local file box. Click the submit 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 submit. If you simply wish to preview the contents of the file in your browser window, leave the file name blank and click submit.

How to back up text-based Custom Track data to a file

• Save Custom Tracks. Save a backup of your current browser sessions's custom tracks to your local machine. This backup is intended to be used to restore uploaded text-based custom tracks that would otherwise be lost in case of an unexpected system failure at UCSC. Saving your data is easy and ensures that your hard work is safe and recoverable. To download your custom track data, navigate to the Save Settings section. Click the submit 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 create custom track backup archive 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 download backup archive 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 return 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.
• Restore a Custom Track. The downloaded archive file cannot be directly reloaded into the system because it is compressed. To reload custom tracks, untar the downloaded .tar.gz file. The following example assumes you named your archive file 'someproject'. From the command-line, change into your Downloads directory, make a directory for your session, and uncompress your custom track archive.

  cd Downloads
  mkdir someproject
  cd someproject
  tar -xzf ../someproject.tar.gz

  If you use the Safari browser, your file will have been uncompressed automatically, leaving just .tar. If this is the case, use this command instead:
  

  tar -xf ../someproject.tar

  The assembly directory contains .ct files, one for each custom track. To restore a single custom track, go to the Custom Tracks tool, select the correct genome database, and click the add custom track button. If you already have existing custom tracks, click the add custom track button, then click the Choose File button next to the top window near the "Paste URLs or data" text. A file selection box will open. Navigate to the directory where the desired custom track .ct file is, choose it, and click the Submit button.
  
  If an optional help text or HTML page was saved with the custom track, you will see a corresponding custom track .html file. You can restore this by selecting the Choose File button near the "Optional track documentation" text. A file selection box will open. Navigate to the directory where the .html file is located, choose it, and click the Submit button.
• Restore Multiple Custom Tracks. Restore all the custom tracks in an assembly directory by concatenating the .ct files together. From the command-line, change directory to your genome assembly and concatenate all of the .ct files into on hg38_all.ct file:

  cd hg38
  cat *.ct > hg38_all.ct

  Compress the concatenated file for faster upload, creating hg38_all.ct.gz with the following command:

  gzip hg38_all.ct

  Navigate to the Custom Tracks tool and select the big concatenated compressed file (hg38_all.ct.gz in our example). Note that large custom track sets may require a long time to upload. Once uploaded, click the Go button on the next page to view your custom tracks in the Browser. You will still be able to save and share your Sessions online, which will include your Browser Settings and Custom Tracks. This feature is solely for backing up Custom Tracks as files.

Creating a session — video demonstration

Visit our YouTube channel for more videos.

Opening a saved session

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:

• Session name. Click the session name to view it in the Genome Browser.
• View/edit details. Click the details button to edit the session description and view session details such as creation date/time, assemblies with custom tracks and more.
• Delete the session. Click the delete button to permanently remove this session from the list.
• Share with others: Check this box to allow others to access this session. By default, this option is unchecked, which limits access to only the session owner.
• Post in public listing: Check this box to add your session to the list of Public Sessions. Sessions in the listing will be available to be loaded and viewed by the world.
• Email. Click this link to email this session to a colleague.

Session details

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.

Sharing a session

Shared vs. non-shared data

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:

• the user name and session name of the saved session
• access privileges to a local file that contains the saved session information
• the URL of a web-accessible session settings file

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.

Sharing your session with others

There are five ways to let others know about your saved sessions:

• Save the session URL. Immediately upon saving a new session, the top of the page offers a 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 a session link. Each session entry in the My Sessions list also has an 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.
• Share a session settings file. If you have saved your settings to a local file, you can give others access to the file, or email the file to them as an attachment and instruct them to load it using the Session tool.
• Share a web URL. If you have saved your settings to a file on a web server, you can provide a link like this 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.

• List it on the Public Sessions page. The "Public Sessions" tool allows you to post and share your exciting and interesting Browser snapshots with the world. After having saved your session, you can add it to this public listing by checking the box in the column under "post in public listing?".

Opening a shared session

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.

• Open a session from an email link. If you receive an email message with a link to a colleague's shared session, simply click on the link to view the Genome Browser with the session settings.
• Open another user's session. If you know the name of another user's shared session you can type in the user and session name in the "Restore Settings" section and click "submit" This will generate an "Updated Session" message and you can click on the Browser link to load the browser with the settings saved in this session.
• Open a session from a settings file. Open the Session tool, then scroll down to Restore Settings in the Session Management section. Click Choose File to find the file on your computer. Click submit to display the Genome Browser using these session settings.
• Open a session specified by a URL. Open the Session tool, then scroll down to Restore Settings in the Session Management section. Type in the URL in the Use settings from a URL box, then click submit to display the Genome Browser using the new session settings.

Editing an existing session

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.

Displaying your own tracks in a session

In addition to displaying standard UCSC tracks in your session, you can also display the following user-generated tracks:

• Custom Tracks
• Genome Graph 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.

Deleting a session

In the Session Management section under My Sessions, press the delete 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.

Lifespan of a session

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.

Session gallery

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.

Help for Nucleic Acids Research submitters

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.

Viewing your data on the Genome Browser

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:

1. Ensure the data file is formatted correctly.
2. Create a track line for your custom track.
3. Load the custom track by adding your track line to our Custom Tracks page.
4. View the data in the Genome Browser.

Custom track examples

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:

BAM custom track

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.bam

In 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.bam

There 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.

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bigWig custom track

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.bigWig

There are also options to configure the display of your wiggle tracks, such as changing the track height or type of graph.

Creating a session for NAR publications

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:

1. Configure the Genome Browser to your preference
   Make sure the display of your custom tracks is to your liking on the Genome Browser.
2. Navigate to the sessions page
   Once you are satisfied with the display, go to the My Sessions page by either:
   • Going to My Data -> My Sessions from the navigation bar.
   • Using the "s then s" keyboard shortcut when viewing the main page of the Genome Browser.
3. Login to the UCSC Genome Browser
   You must sign in to be able to save named sessions which will then be displayed with Browser and Email links.
4. Save your session
   Go to the Save Settings section and in the Save current settings as named session text box, enter a name for your session. When saving the session, be sure to have the "allow this session to be loaded by others" option checked and then click submit.
5. Edit the session description
   Once the session is created, you can click the details button to add a description to the session. If you eventually make a Public Session, and provide a detailed description, anyone can find it by searching for terms you share. For example, navigate to the Public Sessions page and search "NAR" to see some example sessions.

Sharing your session link

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:

1. Immediately after creating a new session, the top of the page offers a Browser hyperlink that will allow you to view the newly saved session. You can right-click the Browser link to save the URL.
2. Alternatively, you can right-click the session name and then click Copy Link Address to save the session URL.
3. Adding your session to the Public Sessions page will provide a useful way of sharing your session with the world in the long run. You can add your session to our Public Sessions by selecting the "post in public listing?" checkbox.

Editing the session URL

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.rela

Having hgTracks in the session URL will take the viewer to the main page of the Genome Browser instead of the sessions page.

Using track hubs to organize custom tracks

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.

Genome Browser inquiries

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.