View source for V23: custom categorical track

'''''Saturday, August 3, 2013'''''


The categorical track represents categorical information along the chromosome sequence. Typical example is [http://epigenomegateway.wustl.edu/browser/?genome=hg18&hmtk=wgEncodeBroadHmmNhlfHMM,wgEncodeBroadHmmNhekHMM,wgEncodeBroadHmmK562HMM,wgEncodeBroadHmmHuvecHMM,wgEncodeBroadHmmHsmmHMM,wgEncodeBroadHmmHmecHMM,wgEncodeBroadHmmHepg2HMM,wgEncodeBroadHmmH1hescHMM,wgEncodeBroadHmmGm12878HMM&gftk=refGene,full&metadata=Assay,Sample,Institution&coordinate=chr7:27028917-27318541 Chromatin State (chromhmm)], as shown in following example:

[[File:V23-_custom_categorical_track_1_1.png]]

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":

[[File:V23-_custom_categorical_track_2_1.png]]

You will see the track submission interface:

[[File:V23-_custom_categorical_track_3_1.png]]

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