General Function Checklist

1. Download and

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1. 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.

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2. Select Manage Repositories...

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2. Click Add...

   In the Add Plugin Repository window enter the following information:

   1. 1. Name: Quickload Saver Repo
      2. URL: https://bitbucket.org/lorainelab/quickload-saver/downloads/
   2. Click Submit.
   3. Click Done.

   

   In the Preferences window App Repositories tab:
   Click Done

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   In the IGB App Manager window:Image Added

   • Checkpoint:
   •  mac
   •  linux
   •  windows

   
   

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

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   • Checkpoint:
   •  mac
   •  linux
   •  windows

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   1. Close the IGB App Manager window.

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   2. Select File > Open Genome from File...

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   1. 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
   2. Click OK.
   3. Select File > Open File...
   4. Select E_unicornis_Jul_2043.bed.gz
   5. Click Open.
   6. In the Data Access tab

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   1. 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

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   1. .
   2. Select File > Open Genome from File...

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   1. 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:

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   1. 1. June 1993
   2. Click OK.
   3. Select File > Open URL...

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   1. Enter URL: http://igbquickload.org/quickload/S_cerevisiae_Apr_2011/S_cerevisiae_Apr_2011_ncbiRefSeq.bed.gz

   ...

   2. Click OK.

   In IGBImage Added

   • Checkpoint:
   •  mac
   •  linux
   •  windows

   
   

   In the Data Access tab in the Data Management Table sectionat 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.

   In IGB:

   1. Select File > Preferences...
   2. In the Preferences window select the Other Options tab.
   3. Click Reset Preference to Defaults and then click Yes

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   1. . IGB will close.

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   1. Start IGB

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   1. .
   2. Select File > Preferences

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   1. .
   2. Select the Data Sources tab.

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   2. Click Add...
      

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

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   1. Click Submit

   In the Data Sources tab:Image Added

   • Checkpoint:
   •  mac
   •  linux
   •  windows

   
   

   1. Click Add...

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   1. 
      
      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.

   

   In the Add Data Source tab:
   Click Submit

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   • Checkpoint:
   •  mac
   •  linux
   •  windows

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   1. Close the Preferences window.

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   1. Select the Log tab and click Clear.

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   1. Open the E_unicornis_Jul_

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   1. 2043 genome.
   2. In the Data Access tab, E_unicornis_Jul_2043.bed.gz should be set to Load Mode Genome and should be red (FG).

   Image AddedCompare your

   • Your IGB appears to

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   • look the same as the above image.
   •  mac
   •  linux
   •  windows

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

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   • Your IGB appears to

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   • look the same as the above image.
   •  mac
   •  linux
   •  windows

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   Select the Log tab and check for errors.No

   • There are no errors in the Log

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   • .
   •  mac
   •  linux
   •  windows

   
   

   1. Click Clear in the Log tab

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   1. .

   ...

   1. Open the T_rex_Jun_

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   1. 1993 genome.
   2. 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 Image Added

   • Your IGB appears to

   ...

   • look the same as the above image.
   •  mac
   •  linux
   •  windows

   Image Removed
   

   
   

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

   Compare your Image Added

   • Your IGB appears to

   ...

   • look the same as the above image.
   •  mac
   •  linux
   •  windows

   Image Removed
   

   
   

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

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   1. .
   • There are no errors

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   • in the Log

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   • .
   •  mac
   •  linux
   •  windows