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 tocontact us.

Step 2: Choose species and genome version

There are many species and genome versions in IGB. You can:

  • Click a start screen shortcut image.

These species will automatically load the most current reference annotations

IGB showing the H. sapiens RefGene models

  • Choose Species and Genome Version using the Current Genome tab.

If your genome is not listed, skip to Step 3.

Step 3. Choose data sets

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

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 

Reference sequence

If you have a reference sequence in the fasta, 2bit, or bnib format, File > Open Reference Sequence... will put the sequence in the Coordinate Axis in the center of the display (after Load Data button is used).

Step 4: Click Load Data button

  • If large data sets are selected, zoom to a smaller region (See Step 5)
  • Click Load Data button (green arrow, box in above image).

This will load and draw the data and sequences that you have selected in the Main View.

Step 5: Zoom in

  • Use the zoom slider. (purple box/arrow).
  • Search for a gene. Use the Advanced Search tab, double-click result to jump to a feature (red box/arrow).
  • Enter coordinates in the range box. (green box/arrow).
  • Click-drag within the coordinate axis. (blue box/arrow).
  • Use keyboard shortcuts. Use control+mouse wheel (Windows) or command+mouse wheel (Mac) (yellow box/arrow).

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:

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