General Function Checklist

•  Bookmarks can be created using the Bookmarks menu.

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1. Open the A_thaliana_Jun_2009 genome.
2. Navigate to Chr1:29,253,040-29,260,215
3. Select Add Bookmark from the Bookmarks menu at the top of IGB, then click OK.

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• A new bookmark has been created

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• in the Bookmarks tab.

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•  Bookmarks can be created using the Bookmarks tab.mac
•  linux
•  windows

1. Navigate to the following location on a different chromosome: Chr4:7,149,713-7,153,870
2. Select Add Bookmark from the Bookmarks tab .

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1. on the right side of IGB.
2. In the Name field, paste the name of the gene of interest: AT4G11900
3. Click on Position Only if it's not already selected, then click OK.

• A new bookmark has been created

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•  Bookmarks can save position only.

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•  Observation: Your saved bookmark navigates to your bookmarked position when clicked.

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•  Bookmarks can save position and data. 
  1. Create a bookmark and save Position and Data from the New Bookmarks Window
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  •  Observation: Your saved bookmark navigates to your bookmarked position containing your bookmarked position and all of your bookmarked data.

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•  Bookmark folders can be created using the Bookmarks tab.

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• in the Bookmarks tab.

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•  mac
•  linux
•  windows

Double click on the A_thaliana_Jun_2009, Chr1:29,253,039-29,260,214 bookmark you created earlier.

• IGB's main view is now centered on the bookmarked gene of interest on Chromosome 1 at the correct coordinates.

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•  mac
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1. Navigate to the following gene: ARR15
2. Within the Available Data section, add the LD1 and LD2 tracks from ChIP-Seq > CCA1_ChIPSeq > Reads.
3. Click Load Data.
4. Create a bookmark:
   1. Name: ARR15
   2. Comment: Type-A response regulator; negative regulator of cytokinin signaling. RNA-Seq suggests it is up-regulated by cold.

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1. Click Position and Data, then click OK.
2. Restart IGB.

• All three bookmarks have persisted in the Bookmarks tab after restarting IGB.

•  mac
•  linux
•  windows

Click on the ARR15 bookmark in the Bookmarks tab from IGB's home page.

• Clicking on the ARR15 bookmark opened the A_thaliana_Jun_2009 genome.

•  mac
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•  windows

• The ARR15 bookmark zoomed to the correct coordinates (Chr1:28,131,446-28,133,025).

•  mac
•  linux
•  windows

• The LD1 and LD2 track data was automatically loaded.

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•  mac
•  linux
•  windows

• The ARR15 bookmark's Comment is still present in the bookmark panel after restarting IGB.

•  mac
•  linux
•  windows

Click on the AT4G11900 bookmark.

• The LD1 and LD2 track data is not loaded because this bookmark was Position Only.

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•  mac
•  linux
•  windows

Add a bookmark folder using the Bookmarks tab.

• Your bookmark folder appears in the Bookmarks tab.

•  Bookmarks can be placed into Bookmark folders mac
•  linux
•  windows
  
  

Add the AT4G11900 bookmark to the bookmark folder you've just created.

• The AT4G11900 bookmark was successfully placed into a bookmark folder.

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• mac
•  linux
•  windows

1. Add two new separators in the Bookmarks tab.
2. Move one separator between the first two bookmarks you created.
3. Move the other separator underneath the AT4G11900 bookmark in its own folder.

• Bookmark separators can be placed between bookmarks and bookmark folders.

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•  mac
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•  windows

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Delete the A_thaliana bookmark from the Bookmarks tab.

• Bookmarks, Bookmark folders, separators can be deleted using the Remove a bookmark button.

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•  mac
•  linux
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Restart IGB.

• The A_thaliana bookmark did not come back after deleting it and restarting the IGB session.

•  A  mac
•  linux
•  windows

Copy the ARR15 bookmark's URL

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using Copy Bookmark as URL (found in the Bookmarks menu), then paste it into a web browser.

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• The bookmark's URL can be pasted into a web browser and the web browser navigates to the bookmark in IGB.

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OTHER CHECKS:

•  Bookmarks persist after restarting an IGB session.

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•  Bookmarks persist after resetting IGB preferences to default through the Other Options tab in Preferences.

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•  mac
•  linux
•  windows

1. Rename the AT4G11900 bookmark to the following: Gene of interest, Feb 2024 (AT4G11900)
2. Add the following comment to the AT4G11900 bookmark: Take a look at this gene in more depth for our upcoming study!

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• The AT4G11900 bookmark was renamed and commented on without issue.

•  mac
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•  windows

Export the Gene of interest, Feb 2024 (AT4G11900) bookmark by clicking Export Bookmarks... in the Bookmarks menu

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To save a copy of the bookmarks to a file

• Choose Bookmarks > Export Bookmarks...
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and saving it to your computer.

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• The Gene of interest, Feb 2024 (AT4G11900) bookmark was exported without error.

•  mac
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• The Gene of interest, Feb 2024 (AT4G11900) bookmark was saved as a single file in an HTML-based format.

•   Bookmarks can be imported usingmac
•  linux
•  windows

Select Import Bookmarks... in the Bookmarks menu

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To import another user's bookmarks

• Choose Bookmarks > Import Bookmarks...
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•  Observations: Imported bookmarks will be added to the end of the list of existing bookmarks.

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at the top of IGB and import the Gene of interest, Feb 2024 (AT4G11900) bookmark that you just saved in an HTML-based format.

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• The Gene of interest, Feb 2024 (AT4G11900) bookmark imported without error.

•  mac
•  linux
•  windows

Reset IGB preferences in the Other Options tab in Preferences and reopen IGB.

• Both bookmarks persisted in the Bookmarks tab after resetting IGB preferences.
  

•  mac
•  linux
•  windows

Post-release testing

 Bookmarks are preserved when updating to a new version of IGB.

•  Bookmarks created during this checklist navigate to the proper location in IGB.
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•  linux
•  windows