v19: navigation and apps buttons, adjust browser panel width

This version of our code release features more easily accessible buttons for navigation and apps functions. In the past these buttons are in the floating toolbox, but now they are fitted into the header of browser panel:

The group of buttons on left (in red enclosure) are navigation buttons, they are:
+: zoom in 1 fold
-1/3: zoom out 1/3 fold
-1: zoom out 1 fold
-5: zoom out 5 fold
<: pan left
>: pan right

The group on right (in blue enclosure) are application buttons:
Tracks: click to access the collection of tracks for this genome, including experimental assay tracks and annotation tracks
CustomTK: custom track submission and management interface
Apps: list of applications
Gear button: options for adjusting browser panel width

Please note that the red and blue enclosure are only for screenshot highlighting.


A similar set of buttons is available for secondary panels.

To adjust browser panel width, click Gear button (⚙) to show the options:

Click  in the first row, an orange pane appears covering the browser panel, as an indication of the perspective dimension to adjust to:

Then press to apply the new width.

The second rows of buttons are used to adjust the strip of space on the left of browser panel (where track names are shown).

Download from our server, or dropbox.

v18: new page look, BAM file support

Version 18 code release features a lot of improvements, including new look of user interface throughout the entire browser, and most importantly, the support of BAM files.

You can get the source code from dropbox, or from our web site.

BAM file support

Open up the browser and click "CustomTk" button in the toolbox to show this:

Click button "BAM" to and we're ready to submit a custom BAM track:

Enter URL and track name, and press  . Following shows the display of sample BAM track of human hg19 genome:

Clicking on a read will invoke a bubble showing detailed info about the read, including its alignment:

Showing a paired-end sequencing assay result, where reads mapped on forward strand are in  teal , and reads on reverse strand are in  fuchsia . Mismatches are in  yellow . Clipped bases are in  gray .

Details about mismatches, insertion, deletion, clipping can also be viewed in the bubble. For instance:

A BAM track can also be submitted via URL parameter, and also through data hub.

For instance, the following URL displays a BAM file in hg19 genome:

http://epigenomegateway.wustl.edu/browser/?genome=hg19&custombam=sample+BAM+track,http://vizhub.wustl.edu/hubSample/hg19/bam1.bam,thin


Finally, the SAM files are no longer supported.


Credit: Chee-Hong Wong

New user interface

v17: Circlet View

This code release features improved Circlet View, now a fully interactive, exploratory tool to visualize long-range chromatin interaction data. It achieves the awesome visual effect of the "Circos plot", yet it is so much easier to work with.


You can download the source code from our server, or dropbox.

Trivia

The Circlet View function was made as part of long-range chromatin interaction visualization functionality a while ago (as seen in version 7 code release). Yet we didn't describe it on our blog then, and now that the paper is about to come out, we thought we'd better give it a formal announcement.

This function used to go under name "henge view", and one of our reviewers suggested we'd better change it... so there you go: Circlet.



 Invoke Circlet View 

To invoke the Circlet View, first you need to display a long-range interaction track, e.g. the following example (click here to view in browser):

Right click on the long-range track image and select "Circlet View":

The Circlet View panel will be displayed:

In this example more than one chromosomes are shown in the view (chr10, chr17, chr6, chr1). Each is identified by a blue button. The position of the button pinpoints the start of the chromosome, which means the clockwise direction is 5' to 3' on chromosome sequence.


 Rearrange chromosomes  

To move chr10 to overpass chr17 in this example, press on chr10 button and drag down, orange arc highlights the suggested position of chr10:

After moving sufficient distance, chr10 will swap its position with chr17:

 Zoom in & out 

By default the whole chromosome is shown. You can zoom in and show only a sub section by dragging on chromosome bar:

Following shows updated graph with partially shown chr10 (the region where all arcs originates from):

To zoom out, right click on chr10 name button and press "Zoom out" option:

 Configure rendering style 

Right click on white space of the graph to invoke the configuration panel:

By right clicking on chromosome bar, you will see a list of chromosomes used in the view. This is primarily for adding a chromosome back after you got it removed.

 Add "wreath tracks" 

At the top of the graph click  , a list of currently displayed tracks in the browser is shown:

Here I click tracks "RefSeq genes" and "GC percent" to add them to my current view:

The gene track is displayed as density (green), and GC percent track is in blue.

To configure a track, right click on a track to get the options:

We love this function and hope you can find it useful. We will continue to work and improve it:

1. Remedy the limit of showing regional data only. We will allow you to display Hi-C data on full chromosomes, or even the whole genome, as easy as above steps.
2. You will be able to overlay two tracks inside the same plot and show them as separate colors to compare.
3. SVG output.
4. Make it a plug-in web app. Think about displaying an interactive Circlet plot in your webpage, isn't that cool?