v23: custom categorical track

The categorical track represents categorical information along the chromosome sequence. Typical example is Chromatin State (chromhmm), as shown in following example:

Now you can display your own track data in the form of custom categorical track, for instance you might show various types of SNPs in different colors.

To prepare categorical track, convert your data into a text file with 4 columns in each row. The columns are:

1. chromosome name
2. feature start coordinate
3. feature stop coordinate
4. category ID

Category ID is positive integers starting from 1. Each integer corresponds to a category and will be rendered using its own color.

Compress and index this text file:

$ bgzip myfile.txt
you got "myfile.txt.gz"

$ tabix -p bed myfile.txt.gz
you got "myfile.txt.gz.tbi"

Put both "myfile.txt.gz" and "myfile.txt.gz.tbi" on the same directory of a web server.

Go to the browser, click "CustomTK" and then "Add new tracks", from the list of custom track types, push the button labeled "Categorical data":

You will see the track submission interface:

Enter URL to the file "myfile.txt.gz" or something, and name this track.

Also specify how many categories are there in your file. From the list of text boxes, enter name of each category, and choose a color.

Then click Submit to show this track on the browser.

Once displayed, you can right click on your categorical track and see the list of categories, or change color setting.

The custom categorical track can be saved and restored as session.


Version 23 source code is available from:
http://epigenomegateway.wustl.edu/info/source/
https://dl.dropboxusercontent.com/u/6959481/subtleKnife.v23.tgz

v22 (3 of 3): better track search, and information display

Track search

You can quickly find track using the track search. On browser, click "Tracks" and find the search box:

Enter keywords and press "Search" or hit Enter. To use multiple keywords, join them by "AND".

The search will turn up not only experimental assay tracks, but annotation tracks (e.g. genes or repeats), and tracks from your datahub or custom tracks. Track must be labeled with corresponding keyword or annotated using a matching metadata term to be found out.

Track information display

To see information of a track, right click and select Information:

Track information will be shown as various categories:

Gray boxes in the top row are metadata terms used to annotate this track. Click a term to show its hierarchy in the controlled vocabulary:

v22 (2 of 3): public datahubs

From version 22 the browser is now equipped with "Public Datahubs", which are in-house curated datasets that contain publicly available assay results of high scientific value and interest to the research community. The Public Hub is in the form of datahub, which is independent from the browser track database, and can be hosted on any web server on the Internet.

A pilot release of Multiple Myeloma genomics sequencing results is available as an hg18 public hub in the human genome. The data is provided by James Bradner's lab at Harvard Medical School.

To see the public hub listing for a genome, click "Track", then "Experimental assay tracks". The Experimental Assay Track panel will be shown. Click tab "Public datahubs" to show the listing:

We would love to publish your data! Please feel free to contact us at epigenome@lists.genetics.wustl.edu