IGB User's Guide
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Introduction

Reference

As you get to know IGB, you'll find it offers many features designed to enrich your genome browsing experience.

However, most of us want to 'jump right and make it work' and don't need to explore these many features right away.

Here we provide a brief Quick Start Guide to help you get started using IGB.

Step 1: Download and start IGB

1. Go to bioviz.org/igb and click Downloads.

2. Click the IGB image to download and launch IGB. If your computer has enough memory, we recommend choosing the high memory (2 or 5 GB) option.

IGB Download Page - Small, medium, and large memory options

Step 2: Choose your species and genome version, if available

  • Click an image or choose species and version under the Current Genome tab (blue box). 
    • For some species, gene models and cytological bands will automatically load.
  • If your genome of interest is not listed, don't choose anything and skip to Step 3.
IGB start screen

IGB after selecting the latest human genome. RefSeq alignments are show in blue.

Step 3. Load data sets from Data Source servers

  • Select and load annotations
    • Open data source folders under the Data Sources and Data Sets file tree (red box)
    • Select data sets you would like to view by
      • checking the box
      • or click-dragging them into the Data Management table

When you select a data the data sets you would like to load, IGB will add new track (orange box) to the main viewer.

To view data

    • Zoom or scroll to a region of interest
    • Click Load Data (green arrows, boxes) to load data into IGB

Step 4: Load data from local files

To view data from local or remote files

  • Use File > Open... or File > Open URL... to select a file or
  • Click-drag the file or Web link into the IGB main viewer

When you open a file, IGB adds new track to the main view. 

Areas that are NOT loaded are grayed out (as you can see in the place holder tracks).

and adds the file to the list of active data sets in the Data Management Table.

To load data into the main view, click Load Data.

Note: Many data files (especially BAM files) are huge and contain too much data to display at once. For this reason, IGB does not automatically load data from a newly opened file. To view data in a file, zoom and scroll to a region or gene of interest and click Load Data. IGB indicates regions that have not yet been loaded by displaying a slightly darker background color.

Reference Sequence

If you have a sequence file (fasta, 2bit, bnib, etc.) that you would like to use as the reference sequence, use the File > Open Reference Sequence... option.

Step 5: Zoom in on a region of interest

If you're working with large files such as .bam, .sam, .wig, .bedGraph, you should 'zoom in' to a smaller area before loading your data, i.e. select a smaller region of data to load. To zoom in on a region of interest, you can:

  • Use the zoom slider to zoom in on a gene (purple box/arrow). Click in the main window to focus zooming and then drag the slider to right to zoom in.
  • Click the Search tab and enter the name of a gene.  Double-click rows in the results list to jump to a feature (red box/arrow).
  • Double click on a feature within the visual field to zoom to that feature (orange box/arrow).
  • Enter a coordinate range in the coordinate box and hit enter to zoom to that location (green box/arrow)
  • Click and drag within the coordinate axis to zoom to a region of interest (blue box/arrow).


See also:

Step 6: Configure tracks

You can change track color, how IGB indicates strand, track labels, and much more.

To change track appearance

  • Right-click (or control-click on Mac) a track label and choose Change or Configure.. options
  • Click File > Preferences
  • Click a color swatch in the Data Management Table

See also:

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