Use the Browser

The Top Menu

The top navigation menu (above) controls most of the browser functionality. From left to right are the browser logo with version information, species and assembly information, genomic region locator, zoom in/out tools, Tracks menu, Apps menu, Settings menu and Documentaion link.

Genomic Region Locator

The genomic region locator allows the user to navigate to a region or gene.

Gene Search

You can type a gene name/symbol, like Hox, and when the input content reaches 3 characters the browser will try to find gene symbols starting with what you typed:

After a gene is selected a dropdown menu will pop up with isoforms for the gene. After clicking an isoform the browser will navigate you to its genomic region.

Voice input gene symbol

From this set of buttons, , click the Say a Gene button, your web browser will ask you for permission to access your microphone devices, choose Allow, and the browser will start to listen to what you are saying. You can start saying letters one by one, like H, O, X, if you click the red stop button, what you said “HOX” will populate the gene search box and suggested gene symbols will pop up. As before you can then choose the gene and isoform you want to navigate to.

Note

This feature is dependent on web browser support. A web browser without support for speech recognition won’t see this UI.

SNP search

SNP search is also avaiable from the genomic region locator button:

say you input a SNP id: rs1259546924, click the Go button, you will get information about this SNP:

Click the blue postion link can navigate you to this SNP’s position:

Note

SNP search uses the Ensembl API services: https://rest.ensembl.org

Region Search

Below the gene search box you can use the region search box to navigate to specific genomic coordinates. Formats such as chr6:52258852-52260880 or chr6 52258852 52260880 are accepted (the browser is not sensitive to the number of spaces or tabs between the chr, start, and stop.

Operations in the Tracks View Container

Right above the tracks on the left hand side there are a bunch of tools for operating on the tracks. From left to right these include the move, re-order, zoom, undo, redo, and history tools.

Move/Re-order/Zoom tools

The is the default tool selected by the browser. Moving mode allows the user to drag the mouse right or left and the tracks will move along mouse moving to new regions. The allows tracks to be re-ordered. The user can drag one or more tracks up or down to change the order of tracks. The allows the user to zoom in on a specific region within the current view using the mouse.

Undo/Redo/History tools

contains the Undo, Redo, and History tools. For instance if you accidently moved to another region and forgot what you were looking at before you can click the Undo button to go back. Clicking the Redo button allows you to go forward to the step before you clicked Undo. The History button gives you the 9 most recent operations and allows you to jump to any of these operations or clear the history.

Hotkeys

1. Alt + H or Alt + D for the Drag Tool

2. Alt + S or Alt + R for the Reorder/Swap Tool

3. Alt + M for the Magnify Tool

4. Alt + Z and Alt + X to pan one full panel left or right.

Settings

The Settings menu controls global settings for the browser.

Toggle display of the Genome Navigator

By using the genome navigator (below) users can jump to any genomic region or chromosome(s).

The operations on the genome navigator are:

• Left mouse drag: select

• Right mouse drag: pan

• Mousewheel: zoom

The genome navigator can also be hidden to save space when viewing tracks. Click Settings on the top menu and uncheck the box to switch off this feature:

Toggle highlighting of enter region

When a user jumps to a region or gene using the Genomic Region Locator, that region or gene is highlighted with a light yellow box.

This highlighting can be turned off/on by clicking the botton on the Settings menu:

Change track label width

The default width of track labels (below) is 120 pixels.

The width of the track label can be configured by the submenu under the Settings menu:

Toggle display of VR mode

From the Settings menu the user can choose to toggle the VR display mode of tracks:

After choose the Show 3D scene submenu, a new container with VR view of the tracks will appear:

You can click the icon at the bottom right to toggle the full screen display of VR mode, then you can use your mouse and keys W, A, S and D to control the view of VR mode, like this view below can show you the interaction between two genomic loci and methylation status along this region in a 3D way.

Apps

Region set view

Users can submit a list of regions or genes to the browser, by choose Apps -> Region set view:

The brings up the region set user interface, here you can enter a list of gene names or coordinates to make a gene set one item per line. Gene names and coordinates can be mixed for input. Coordinate string must be in the form of “chr1:345-678” fields can be joined by space/tab/comma/colon/hyphen.

After Click the Add button, will bring you to the region set editting interface, you can either add region one by one, or delete regions from the table, and set the flanking region strategy:

Once you done with edit the set, cick the button Add set. Now you have the option to enter regin set view, click the button Enter region set view:

This indicates you are in region set view mode and which set you are viewing:

Go back to the browser, you can your browser view is ordered by your region set:

Geneplot

Geneplot function allows users to see overall signal of a numerical track over user selected gene/region sets. Choose Geneplot from the Apps menu, if there is no region sets added before, the browser will bring the region set adding interface:

After adding a region set, you can choose the available set from the dropdown in first step:

Now you need to choose a numerical track, you can use your custom track or publicly avaiable tracks:

After choose a numerical track, click the Plot button, this will generate the boxplot by default:

Choose line plot:

Choose heatmap:

When you mouse over the plot, there is a button for you to download the plot as SVG file:

Session

Choosing Session from the Apps menu will bring you to the session interface shown below:

Save session

Click the Save session button to save a session. A session bundle Id will be created which allows the user to retrieve their session at a later date.

Retrieve session

The session bundle Id can be used later to retrieve a session by pasting the session bundle id in the session interface and clicking the Retrieve session button.

Choose which session status you want to restore:

Click the green Restore button and your session will be restored:

Download and Upload session

Sessions can be downloaded to a json file to your local disk, or can be uploaded from your local drive as well.

Note

The downloaded session file can be put in a URL, then use sessionFile parameter for fast retrieve the session, like http://epigenomegateway.wustl.edu/browser/?sessionFile=https://wangftp.wustl.edu/~dli/test/eg-session--1692c5f0-c392-11e9-829c-912864922e1e.json

Live browsing

From the Apps menu choose Go Live, the browser will navigate you to a new link which you can share with someone else, like your collaborator, your PI, or your friends. Whatever operations are done by you are mirrored on the displays of the people who opened the same link.

Screenshot

Users can create publication quality images using the Screenshot tool from the Apps menu. Click the Screenshot button and a new window will po pup that re-renders all your tracks as a new SVG file. Once rendered you can click the green download button to save the current browser view as a SVG image file.

Fetch Sequence

From the Apps menu choose Fetch Sequence,, this function allows user to retrieve genomic sequence of current view region, or users can also specified a list of regions to fetch the sequences. Each region should no longer than 10KB.

Click the Fetch or Batch fetch button to fetch the sequence. Click the Copy button can copy the fetched sequence to your clipboard.

Track management

The browser collects data from large corsortia like Roadmap Epigenomics, ENCODE, 4DN, TaRGET, etc. The data are called public data/tracks and are organized into different collections called hubs. Along with these public hubs and tracks users can submit their own custom tracks and data hubs to allow for easy comparison.

Add tracks from public hubs

From the Tracks menu choose Public Data Hubs. This will display all of the public data hubbs available for the species and build you are currently working in. For example, using mouse mm10 annotation the 4D Nucleome Network hub is available. Click the Add button to load this hub:

After a hub is added, a facet table containing all tracks will pop up. This allows you to choose any tracks you are interested in. The facet table can also be revisted through the menu when you choose Track Facet Table:

You can expand the row and/or column selection by clicking the + buttons. Row and column displays can also be easily swapped:

Clicking a cell within the facet table will pop up a new window containing a table with the tacks that match the row and column selections:

Click the Add button to add the track(s) you want. You can then view tracks in the browser view window:

Adding annotation tracks

Users can add numerous annotation tracks from the Tracks menu by choosing Annotation Tracks.

Each header can be expanded to one or more submenus that display tracks that can be added to the browser. The tracks include CpG island information, repeat information, G/C content information, and conservation information to name a few.

Adding a custom track or data hub

Users can also submit their own track as a custom track. For example, say we have a bigWig track located at https://vizhub.wustl.edu/public/tmp/TW463_20-5-bonemarrow_MeDIP.bigWig . From the Tracks menu choose Custom tracks and a custom track interface will pop up. Fill in the track type, label, and URL before clicking the green Submit button:

You can see the track is added:

Adding a custom data hub is similar to the steps above. For example, say you have a hub located at https://vizhub.wustl.edu/public/tmp/a.json . From the Tracks menu choose Custom tracks, switch to the Add custom data hub tab, paste the URL of your hub, and then click the green Load From URL button. from URL.

The tracks within the custom hub can then be added from the generated facet table.

Note

Tracks from custom hubs are hidden by default as users may submit a hub contains hundreds of tracks. Users should add tracks that they want from the facet table.

You can also load a local data hub file in JSON format from your computer using the file upload interface, right below the URL submit hub interface.

Also see the Tracks and Datahub sections for how to prepare your tracks and datahub files.

Track Customization

Tracks can be customized in a multitude of manners.

Selecting Tracks

An indivdual track can be selected by simply right clicking on the tracking on the track. Multiple tracks can be selected by either holding the shift button and left clicking on each track or by holding shift and left clicking on a shared metadata term of consecutive tracks. In this manner, multiple tracks can be customized or moved at the same time. To deselect the tracks simply right click and press the button Deselect # tracks .

Track Color

Right clicking on annotation and numerical tracks will display Primary Color, Secondary Color, and Background Color which can all be customized using the color picker. For methylC tracks and categorical tracks the Color and Background of each class of elements (e.g. CG, CHG, and CHH) can be personalized. Additionally, for methylC``tracks the ``Read depth line color can be customized.

Track Height

For each track the height can be customized by right clicking on the track and typing in a number to the panel. At 20 pixels and below for numerical tracks the track will display as a heatmap.

Track Display Mode

For each numerical, annotation, or BAM track the display can be changed to DENSITY or FULL mode by right clicking on the track.

Track Y-axis Scale

For each numerical track the y-axis can be displayed in AUTO or FIXED mode by right clicking on the track. The AUTO mode will scale the axis based on numerical values in the immediate area of the view range. The FIXED mode allows the user to select a Y-Axis min or Y-axis max. For values above the set max the Primary color above max can be set for easy viewing. For values below the set minimum the Primary color below min can bet set.

Track Information

If details were specified for a track in the data hub file these can be viewed by right clicking on the sample and clicking on the arrow to the right. An easy access copy but is also available to copy the URL for the track.

Circlet view for chromatin interaction tracks

For any chromatin interaction track type (HiC, longrange, bigInteract), when you right click the track, you can see the Circlet view button:

Click the button will bring you to the Circlet view interface. You can config the layout and/or the data source:

And config the color, scale, flanking region length at each end of one interaction. You also can download the view as a SVG file used for publication.

Offline mode

In case your device goes offline (no WIFI or network is down), the use can still use the local track and local text track function. A notice will show as below to indicate user’s device is currently offline.

New version notice

Whenever there is a new version, a notification will show if user still use the old version.