2015 PAG Computer Demo

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Revision as of 16:11, 5 January 2015 by Elyons (Talk | contribs) (Data Management)

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  • Keynote:
  • PDF:

Register an account/Log in

  • Go to: http://user.iplantcollaborative.org
    • CoGe uses iPlant's Authentication and User Identify Management Service
    • After clicking on the confirmation link provided in the automated email, your account may take a few minutes to propagate to all of iPlant's Authentication Services.
  • Sign-in (link is in top-right of any CoGe page)
  • NOTE: This wiki (CoGePedia) uses a different authentication than CoGe!

Load your own genome

Add Annotations

  • Go to GenomeInfo by pressing "View Genome"
  • Press "Load Gene Annotations"
  • Set a version (e.g., "1")
  • Source: "CoGe" or "NCBI"
  • Leave Restricted
  • Press "Select Data Files"
  • Select "FTP/HTTP" Tab
  • Paste in link below:
  • When the load is finished, pressing "Genome View" will launch the genome viewer (JBrowse).
  • Note: The length of time it takes to load annotations depends on the load on the database and the number of annotations being loaded. For this example (and no load on the server), it should take ~ 3-5 minutes.

Data Management

  • Go to your User Profile page: https://genomevolution.org/CoGe/User.pl
  • Select a genome by clicking on it.
  • Information about the genome will appear in the right panel
  • You can share a genome by clicking on the person icon
  • You can delete the genome by clicking on the trash can
  • Double-clicking the genome will open the Detailed View for it (GenomeInfo)
  • Share it with the person next to you
  • You can view genomes (and other data) that has been shared with you by clicking on "Shared with me" in the menu on the left.

Your History and Activity

  • If you are logged into CoGe, CoGe will record your activities. These are available for review in your User Profile page: https://genomevolution.org/CoGe/User.pl
  • Click on "Activity" in the menu on the left. This will give you an overview of the number of analyses you've run
  • Your previously run analyses can be viewed by clicking "Analyses". Clicking on an analysis will re-run it.

Comparative Genomics

Loading your own genome

RNASeq Processing

CoGe Learning Material