General Function Checklist

1. Download and unzip the following folder: test genomes.zip 
2. The folder "test genomes" should contain the following files:
   1. E_unicornis_Jul_2043.bed.gz.tbi
   2. E_unicornis_Jul_2043.bed.gz
   3. E_unicornis_Jul_2043.2bit
   4. T_rex_Jun_1993.2bit
3. Start IGB 9.1.8 or later.
4. Select the Plug-ins tab.
5. Click Launch App Manager.
6. Select Manage Repositories...
7. Click Add...
   1. Name: Quickload Saver Repo
   2. URL: https://bitbucket.org/lorainelab/quickload-saver/downloads/
8. Click Submit.
9. Click Done.

• Checkpoint:

• mac
• linux
• windows

1. In the Plug-ins tab, click Launch App Manager.
2. Select the Quickload Saver app.
3. Click Install.

• Checkpoint:

• mac
• linux
• windows

1. Close the IGB App Manager window.
2. Select File > Open Genome from File...
   1. Reference Sequence: Click Choose File... and select E_unicornis_Jul_2043.2bit
   2. Genus: Equus
   3. Species: unicornis
   4. Variety: (leave blank)
   5. Genome release date: July 2043
3. Click OK.
4. Select File > Open File...
5. Select E_unicornis_Jul_2043.bed.gz
6. Click Open.
7. In the Data Access tab at the bottom of IGB,
   1. Change the Load Mode to Genome for E_unicornis_Jul_2043.bed.gz
   2. Change the color of the foreground (FG) to red.

• Checkpoint:

• mac
• linux
• windows

1. Select File > Save Custom Genome to Local Quickload Site
2. Select your desktop as the destination and unicorn as the name.
3. Click Save.
4. Select File > Open Genome from File...
   1. Reference Sequence: Click Choose File... and select the T_rex_Jun_1993.2bit
   2. Genus: Tyrannosaurus 
   3. Species: rex
   4. Variety: (leave blank)
   5. Genome release date: June 1993
5. Click OK.
6. Select File > Open URL...
7. Enter URL: http://igbquickload.org/quickload/S_cerevisiae_Apr_2011/S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz
8. Click OK.

• Checkpoint:

• mac
• linux
• windows

In the Data Access tab at the bottom of IGB:

• Change the Load Mode to Genome for S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz
• Change the color of the foreground (FG) to green.

• Checkpoint:

• mac
• linux
• windows

1. Select File > Save Custom Genome to Local Quickload Site.
2. Select your desktop as the destination and rex as the name.
3. Select File > Preferences...
4. In the Preferences window select the Other Options tab.
5. Click Reset Preference to Defaults and then click Yes. IGB will close.
6. Start IGB.
7. Select File > Preferences.
8. Select the Data Sources tab.
9. Click Add...
   
   1. Name: unicorn
   2. Type: Quickload
   3. Click Choose local folder
10. Select the unicorn folder on your desktop and click Open.
11. Click Submit

• Checkpoint:

• mac
• linux
• windows

1. Click Add...
   
   1. Name: rex
   2. Type: Quickload
2. Click Choose local folder.
3. Select the rex folder on your desktop and click Open.
4. Click Submit.

• Checkpoint:

• mac
• linux
• windows

1. Close the Preferences window.
2. Select the Log tab and click Clear.
3. Open the E_unicornis_Jul_2043 genome.
4. In the Data Access tab, E_unicornis_Jul_2043.bed.gz should be set to Load Mode Genome and should be red (FG).

• Your IGB appears to look the same as the above image.

• mac
• linux
• windows

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

• Your IGB appears to look the same as the above image.

• mac
• linux
• windows

Select the Log tab and check for errors.

• There are no errors in the Log.

• mac
• linux
• windows

1. Click Clear in the Log tab.
2. Open the T_rex_Jun_1993 genome.
3. In the Data Access tab, S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz should be set to Load Mode Genome and should be green (FG).

• Your IGB appears to look the same as the above image.

• mac
• linux
• windows

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

• Your IGB appears to look the same as the above image.

• mac
• linux
• windows

1. Select the Log tab and check for errors.
2. Click Clear in the Log tab.

• There are no errors in the Log.

• mac
• linux
• windows