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How to handle assembly changes in UCSC?

Learn how to navigate and manage assembly changes in the UCSC Genome Browser, select and switch versions, customize tracks, export data, and stay updated efficiently.

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How to handle assembly changes in UCSC?

 

Accessing UCSC Genome Browser

 

  • Navigate to the UCSC Genome Browser website.
  •  

  • Ensure you're familiar with the current assembly by checking the homepage for recent updates or changes.

 

Selecting the Genome Assembly

 

  • On the UCSC main page, locate and click on the "Genomes" link to view available assemblies.
  •  

  • Select the desired organism from the drop-down menu to populate the list of available assemblies.

 

Switching Between Assemblies

 

  • Use the assemblies drop-down list found on the genome browser interface to choose a different assembly version.
  •  

  • After selecting an assembly, the browser will automatically reload to reflect the new assembly context.

 

Verifying Assembly Details

 

  • Click on the "Track" settings or the "Assembly" details link if available to get more information about the selected assembly.
  •  

  • Review the provided metadata, including any updates to sequencing data or annotation changes.

 

Customizing Track Display

 

  • Go to the "Tracks" section to modify how data is shown under the selected assembly.
  •  

  • Select or deselect available tracks based on your research focus to customize the display.

 

Exporting Data

 

  • For further analysis, locate the "Table Browser" or download options, which are typically found within navigation menus.
  •  

  • Follow the instructions to export data in formats such as FASTA or BED, ensuring it pertains to your chosen assembly.

 

Maintaining Updates

 

  • Regularly check the UCSC Genome Browser news updates or mailing lists for announcements of new assemblies.
  •  

  • Consider setting up alerts for updates if your research requires frequent utilization of the latest assembly data.

 

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