v30: custom gene tracks

All the gene tracks on the browser have been upgraded to a new format, and supported by a new mechanism. For all animal genomes all the gene track data have been updated with latest downloads from UCSC Genome Browser. A RefSeq genes and "xenoRefSeq genes" tracks are available for every animal genome and provides good annotation coverage, the latter provides homologous genes from other species.

This new gene track mechanism also supports custom gene tracks:

In above image two gene tracks are shown. The one on top is the native hg19 RefSeq gene track. The green track beneath it is an replica custom track. You can see from the details about this track in the menu box.

An example custom gene track can be found in this hg19 data hub, look for the word "hammock":

http://vizhub.wustl.edu/hubSample/hg19/hub.json


This page has some instructions about preparing gene tracks.

Download the browser source code from here or here.

v29 (4 of 4): the methylC track

Version 29 makes official unveil of the "methylC" track, though it has been available on our browser for a while.

The methylC track is able to display single-base DNA methylation data by discerning cytosine context (CG/CHG/CHH), strand-specificity, and incorporating confidence level data.

Thus it is excellent in visualizing whole-genome bisulfite sequencing (WGBS, or methylC-seq) results. In this case the confidence level data is read depth.

Surely it makes same support on Reduced Representation Bisulfite Sequencing (RRBS) results.

It can even be used for array-based methods such as Infinium 450K. In this case the -log10(P-value) will be used as confidence level.

Refer to http://epigenomegateway.wustl.edu/+/cmtk/ for more details.

A manuscript describing methylC track is under preparation.

v29 (3 of 4): delete custom tracks

We brought back a function that allows you to delete custom tracks in your current session.

After you've loaded custom tracks, click "CustomTK" > "List of all":

From the custom track listing you can find a "delete" button following each track. Click this button and the track will be gone, so be careful.

v29 (2 of 4): displaying track hubs from UCSC Genome Browser

From version 29 we make initial support of UCSC track hubs. However due to inconsistency problems the support is partial:

• bigWig and BAM tracks are supported
• VCF track is not supported for the moment
• bigBed is not supported
• information on all composite tracks will be merged into one metadata vocabulary
• only a handful of rendering controls can be parsed for the moment

To see public hub listing on UCSC, go to http://genome.ucsc.edu/cgi-bin/hgHubConnect

Copy a hub file URL (e.g. http://zlab.umassmed.edu/zlab/publications/UMassMedZHub/hub.txt) and enter it into the text field below. Choose "UCSC hub" from the format menu:

Press SUBMIT and accepted tracks will be loaded.

Both hub file and trackDb file can be submitted in this way. Also you can submit a UCSC hub via URL parameter:

http://epigenomegateway.wustl.edu/browser/?genome=hg18&datahub_ucsc=http://smithlab.usc.edu/trackdata/methylation/hub.txt

v29 (1 of 4): access HTTPS resources, including Dropbox

From version 29 you can now access tracks hosted on a HTTPS web server, including those that are publicly shared on the Dropbox.

Submitting an HTTPS track for display is identical as that with an HTTP track:

• submit from custom track panel at "CustomTK" > "Add new custom track"
• submit by datahub
• submit by URL parameter (same parameter names apply for HTTP and HTTPS tracks)
• submit by embedded browser

Try this example: a BAM track from Dropbox

http://epigenomegateway.wustl.edu/browser/?genome=hg19&custombam=dropbox+bam+track,https://dl.dropboxusercontent.com/u/6959481/hg19_test.bam,full

(this BAM track is for testing only and contains just tiny amount of data)




To host a track on Dropbox


You must have the Public folder in your dropbox. But for accounts created after Oct. 2012, you won't have it automatically. You need to create one yourself by following this link: https://www.dropbox.com/help/16/en

• upload your track files to the Public folder (so that they are publicly shared)
• for tabix and BAM files, put the index file in the same folder as track file
• obtain URL link to your track file by right clicking on the file and select "Copy public link"
• don't do this on the index file
• use this URL for track submission

Be aware not to make excessive use of Dropbox-hosted files.

Get the source code (and here) and refer to the new installation instructions.

v28 (2 of 2): track configuration

We've improved the track configuration options to fix bugs and bring more consistent behavior of the browser interface. There's some slight changes to the options shown as below, but now the functions should work more as expected than before.

Following is the configuration options on a quantitative track. You can get a similar looking panel for a feature-density track (e.g. a BAM track in density mode) without the "negative value" color option:

By checking the box for "apply to all tracks", your next configuring action will be applied to all the tracks in the browser (it used to be just those tracks in genome heatmap), well, for all applicable ones. Such that the gene track color won't be changed along if you change the positive value color for quantitative tracks.

Following is configuration options for an long range interaction track:

If you are configuring a long range interaction track in "heatmap" mode, the "height" option will appear. And if the track is in "full" mode, the text options (font size, color etc.) will appear.

Finally, when you have the secondary panel in the browser, any configuration options applied on a track in the secondary panel will be automatically applied to the same track in the main panel.

v28 (1 of 2): multiple track selection

From version 28 it is possible to select multiple tracks using SHIFT-click and operate on the selected tracks as a batch.

Very simply, click on a track while pressing Shift key on your keyboard. The track name background will turn yellow:

Click again on a highlighted track will de-select it. To operate on selected tracks, right click on any one of them and see menu options. You can configure their rendering style (e.g. color and height), or drop them all together.

To cancel the selection, use the "cancel multiple select" option or simply right click on an un-selected track. The yellow highlight color will go away to indicate the cancellation.

You can still drag and vertically reorder a track while it's selected. But you can't move all of them together.

This feature has been tested to work on all major platforms including Windows, Mac, and Linux. Supported web browsers include IE10, Firefox, Google Chrome, Chromium, Safari.

Get the source code of this version from our website or dropbox.

v27 (3 of 3): custom track listing

We brought back a missing feature, which allows you to view the entire list of custom tracks that have been loaded.

Click "CustomTK" button and find the "List of all" option. You need to load a datahub or some custom tracks first or these options won't show up:

Click this option to see a listing of all your custom tracks:

Those ones that are already on display are shown as inactive labels. Click the active ones and select a bunch to display on the browser.

Such track listing function is necessary as it allows you to find tracks that are NOT ANNOTATED by any metadata terms.

Those annotated by metadata terms will show up in the facet table, as described in this post: v24 (3 of 3): facet panel

v27 (2 of 3): make screenshot for Genome snapshot

The Genome snapshot (used to be call "bird's eye view") is often found useful. It is now made more useful with the SVG output.

Simply click the "screenshot" button on top of the panel to do it. A few seconds later a link will appear right next to the button showing you the SVG file.

v27 (1 of 3): GENCODE V17 track for the human genome

GENCODE version 17 of the human genes are now on hg19. Credit goes to UCSC Genome Browser where the data was obtained. GENCODE is one of the most finely curated gene tracks out there, and we're really happy to have it in our Browser.

http://epigenomegateway.wustl.edu/browser/?genome=hg19&gftk=gencodeV17,full

Genes are assigned into 5 categories, distinguished by color:

      coding genes
      non-coding genes
      pseudogenes
      with problem!
      polyA signal

For the "problem" ones, their causes can be seen in the tooltip bubble, such as "retained_intron".

In the tooltip, links are given to the gene model's record in GENCODE database.



This is the start of the effort to improve all the gene tracks on our Browser, including the underlying mechanism. Right now the GENCODE V17 track is new format and is supported by new mechanism, alongside the old gene tracks such as refGene, GENCODE V11.

With the new mechanism we can reduce the dependence on mysql storage and store all the data in the compressed track file, so that the new gene tracks can work as custom tracks. On such basis a new track type is been developed to support the RNA-seq experiments.