IGB User's Guide
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  • Created by Unknown User (rhynwa), last modified on Jan 28, 2013
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Introduction

As you learn to use IGB, you'll find it offers many features that make it one of the best tools available for visualization and exploration of genomic data sets.

If you are new to IGB, the following six step Quick Start Guide will help you get started using IGB.

Step 1: Get and start IGB

If your computer has enough memory, we recommend the 2 or 5 GB option.

If you have trouble starting IGB, see the Troubleshooting page or feel free to contact us.

Step 2: Choose species and genome version

There are many species and genome versions in IGB.

  • Click a start screen shortcut image to automatically load the most current reference annotations
  • Choose Species and Genome Version using the Current Genome tab.

IGB showing the H. sapiens RefGene models

If your species or genome version is not listed, you can still visualize your data as a custom species or genome. Just go on to Step 3.

See also

Step 3. Choose data sets

Available Data folders

Open a folder under the Available Data file tree (red box) and select data sets:

  • Check the box (red arrow)
  • Drag the data set into the Data Management table

Local files

To view data from local or remote files

  • Use File > Open... or File > Open URL... to select a file or enter a URL
  • Drag the file or web link into the IGB window 

When you select data sets or files, IGB adds a new empty track to the main view and lists it in the Data Management table (orange arrows). Since many data files and data sets (such as BAM files) contain too much data to display all at once, you control when and how much data are loaded.

Reference sequence

If you have a sequence in the fasta, 2bit, or bnib format,and you would like to use it as the reference sequence

  • Use File > Open Reference Sequence...
  • Press Load Data button (see Step 5).
  • Sequence will appear in the Coordinate Axis

Step 4: Zoom in

  • Use the zoom slider: Click in main view to set the center of the focused zooming (Zoom Stripe). Use the zoom slider to zoom in or out (red arrow).
  • Search for a gene or region: Enter range values in the range box and hit enter to jump to a specific region. Enter a keyword or gene name into the range box OR use the Advanced Search tab to search for a specific gene model or feature; double-click a search result to jump to that feature (blue arrows).
  • Double click a feature.

 

See also:

Step 5: Click Load Data button

This will load and draw the data sets that you have selected.

See also:

Step 6: Configure tracks

You can reorder the tracks by dragging the Track Label into the position you want (the Data Management Table reflect changes).

The Annotations tab will allow you to change color, size, amount of data shown as well as other various functions.

See also:

Preferences

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