Difference between revisions of "2015 PAG Computer Demo"

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(Load your own genome)
(Comparative Genomics)
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**When finished being retrieved, press "Load Annotations"
 
**When finished being retrieved, press "Load Annotations"
 
* 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 ~ 5 minutes.
 
* 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 ~ 5 minutes.
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===Data Management===
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* Go to your User Profile page: https://genomevolution.org/CoGe/User.pl
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* Select a genome
  
 
===Comparative Genomics===
 
===Comparative Genomics===
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** Search genome of Arabidopsis thaliana: http://genomevolution.org/r/d774
 
** Search genome of Arabidopsis thaliana: http://genomevolution.org/r/d774
 
** Microsynteny analysis: http://genomevolution.org/r/d778
 
** Microsynteny analysis: http://genomevolution.org/r/d778
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===Loading your own genome===
 
===Loading your own genome===
 
* E. coli genome:  http://de.iplantcollaborative.org/dl/d/555B53F9-E738-4951-85A3-421E23804DFA/genome_7112.faa
 
* E. coli genome:  http://de.iplantcollaborative.org/dl/d/555B53F9-E738-4951-85A3-421E23804DFA/genome_7112.faa

Revision as of 14:59, 5 January 2015

Slides

  • 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:
  • 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 ~ 5 minutes.

Data Management

Comparative Genomics

Loading your own genome

RNASeq Processing

CoGe Learning Material