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General Function Checklist

Download and unzip test genomes.zip 

The folder "test genomes" should contain the following files:

  • E_unicornis_Jul_2043.bed.gz.tbi
  • E_unicornis_Jul_2043.bed.gz
  • E_unicornis_Jul_2043.2bit
  • T_rex_Jun_1993.2bit

Start IGB 9.1.8 or later.
Select the Plug-ins tab.
Click Launch App Manager.
In the IGB App Manager window:

Select Manage Repositories...

In the Preferences window App Repositories tab:

Click Add...

In the Add Plugin Repository window enter the following information:

  • Name: Quickload Saver Repo

Click Submit

In the Preferences window App Repositories tab:
Click Done

In the IGB App Manager window:
Select the Quickload Saver app.
Click Install.

Checkpoint:

  • mac
  • linux
  • windows

Close the IGB App Manager window.
In IGB:
Select File > Open Genome from File...

In the Open Genome from File window:

  • Reference Sequence: Click Choose File... and select E_unicornis_Jul_2043.2bit
  • Genus: Equus
  • Species: unicornis
  • Variety: (leave blank)
  • Genome release date: July 2043

Click OK

Select File > Open File...
Select E_unicornis_Jul_2043.bed.gz
Click Open
In the Data Access tab in the Data Management Table section:
Change the Load Mode to Genome for E_unicornis_Jul_2043.bed.gz
Change the color of the foreground (FG) to red


Select File > Save Custom Genome to Local Quickload Site
Select your desktop as the destination and unicorn as the name.
Click Save

In IGB:
Select File > Open Genome from File...

In the Open Genome from File window:

  • Reference Sequence: Click Choose File... and select the T_rex_Jun_1993.2bit
  • Genus: Tyrannosaurus 
  • Species: rex
  • Variety: (leave blank)
  • Genome release date: June 1993

Click OK

Select File > Open URL...
In the Open URL window:
Enter URL: http://igbquickload.org/quickload/S_cerevisiae_Apr_2011/S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz


Click OK
In IGB:
In the Data Access tab in the Data Management Table section:
Change the Load Mode to Genome for S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz
Change the color of the foreground (FG) to green.


Select File > Save Custom Genome to Local Quickload Site
Select your desktop as the destination and rex as the name.

In IGB:

Select File > Preferences...

In the Preferences window select the Other Options tab.

Click Reset Preference to Defaults and then click Yes

Open IGB
In IGB:
Select File > Preferences
In the Preferences window:
Select the Data Sources tab.
In the Data Sources tab:
Click Add...
In the Add Data Source window:

  • Name: unicorn
  • Type: Quickload
  • Click Choose local folder

Select the unicorn folder on your desktop and click Open

Click Submit


In the Data Sources tab:
Click Add...
In the Add Data Source window:

  • Name: rex
  • Type: Quickload
  • Click Choose local folder

Select the rex folder on your desktop and click Open

In the Add Data Source tab:
Click Submit

Checkpoint:

  • mac
  • linux
  • windows


Close the Preferences window
In IGB:
Select the Log tab and click Clear
In the Species dropdown select Equus unicornis
In the Genome Version dropdown select E_unicornis_Jul_2043
In the Data Access tab, E_unicornis_Jul_2043.bed.gz should be set to Load Mode Genome and should be red (FG)

Compare your IGB to the picture below and check the box if they appear to be the same:

  • mac
  • linux
  • windows


Navigate to chrXVI:2,618-2,661
Click Load Sequence

Compare your IGB to the picture below and check the box if they appear to be the same:

  • mac
  • linux
  • windows


Select the Log tab and check for errors.

No errors in Log tab:

  • mac
  • linux
  • windows

Click Clear in the Log tab if there are no errors.

In the Species dropdown select Tyrannosaurus rex
In the Genome Version dropdown select T_rex_Jun_1993
In the Data Access tab, S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz should be set to Load Mode Genome and should be green (FG).

Compare your IGB to the picture below and check the box if they appear to be the same:

  • mac
  • linux
  • windows


Navigate to chrXVI:2,618-2,661
Click Load Sequence

Compare your IGB to the picture below and check the box if they appear to be the same:

  • mac
  • linux
  • windows


Select the Log tab and check for errors.
Click Clear in the Log tab if there are no errors.

No errors in Log tab:

  • mac
  • linux
  • windows



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