UTGB Toolkit User's Manual

This page describes the usage of UTGB Toolkit.

Track frames

Drag & drop of tracks is supported in UTGB, and also you can resize the height of tracks by dragging the lower frame border of the tracks.

Icons

  • http://utgenome.org/UTGBMedaka/image/icon/icon_01.gif Configuration button
    • Opens the configuration panel for the track
  • http://utgenome.org/UTGBMedaka/image/icon/icon_05.gif / http://utgenome.org/UTGBMedaka/image/icon/icon_06.gif Adjusts the height of the track
    • Resizes the track frame height according to the track image size
  • http://utgenome.org/UTGBMedaka/image/icon/icon_02.gif / http://utgenome.org/UTGBMedaka/image/icon/icon_03.gif Minimize/Restore track button
    • Minimizes/Restore the height of the track frame
  • http://utgenome.org/UTGBMedaka/image/icon/icon_04.gif Close Button
    • Closes unnecessary tracks

Keyboard short cuts

The following keyboard shortcuts are provided for relocating the window location quickly:

Left		scroll left
Right		scroll right
Up		zoom out
Down		zoom in

Basics

Tracks displayed in UTGB can be configured by editing config/view/default-view.silk file. Each track configuration enclosed in track node has common parameters, class, name, pack and height. The class parameter must be present to specify a type of the track. Here is an example of a track configuration:

-track 
 # Track types. (e.g., ReadTrack, WigTrack, RefSeqTrack, RulerTrack, etc.)
 # Case differences and spacing will be ignored in this parameter. 
 -class: ReadTrack
 # Name of the track
 -name: BED Track
 # To pack track height. If pack value is true (default), the height of this track will be fit to its content height 
 -pack: true
 # Pixel height of the track. If pack is set to true, this field will be ignored.
 -height: 30
 # Track-specific properties. See the track catalog for details
 -property
  -path: (read file name)

The other parameters are optional but tracks usually have track-specific configuration parameters. For example, ReadTrack requires path value under property node to specify a data source to display. For details, see Track Catalog.

Change the default location to display

To set the default coordinate location in genome to display, use track group:

-track group
  -coordinate
    -species: human
    -ref: hg19
    -chr: chr1
    -start: 1
    -end: 10000

List of available tracks

In UTGB, you can display data written in BED, SAM, BAM, WIG, FASTA format data. See the following page to create tracks for these data formats.

Folder structure

Here is the initial folder strucrture of the web application generated by UTGB shell:

README		Instruction file
config		configuration folder
db		database folder
eclipse		eclipse launch file folder
src		source codes
pom.xml		project description
war		temporary folder for GWT codes; containing javascript codes
target		work folder containing build classes, temporary files

Silk Data Format

Silk is a compact text format for describing biological data.