Page tree
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 158 Next »

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





  • No labels