Difference between revisions of "2015 PAG Computer Demo"

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(→‎Register an account/Log in)
(→‎Load your own genome)
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===Load your own genome===
 
===Load your own genome===
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* Start in  
+
* Start:
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* E. coli genome:  http://de.iplantcollaborative.org/dl/d/555B53F9-E738-4951-85A3-421E23804DFA/genome_7112.faa
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** From your user profile page (must be logged into CoGe): https://genomevolution.org/CoGe/User.pl
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* E. coli annotations: http://de.iplantcollaborative.org/dl/d/C1ACC5C3-1E0B-409B-8A91-C969943F41F8/7122-structural-annotations.gff
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*** Click "Create"-> "New Genome"
 +
*** Go directly to [[LoadGenome]]: https://genomevolution.org/CoGe/LoadGenome.pl
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* Search for Organism "Escherichia coli K12 strain K-12 substrain MG1655" (just type in "MG1655")
 +
* Set a version (e.g., "1")
 +
* Leave "Type:" as "unmasked"
 +
* Source: "CoGe" or "NCBI"
 +
* Leave as "Restricted"
 +
* Press "Add Data"
 +
* Select "FTP/HTTP" tab
 +
* Paste in the link below:
 +
** E. coli genome:  http://de.iplantcollaborative.org/dl/d/555B53F9-E738-4951-85A3-421E23804DFA/genome_7112.faa
 +
* Press "Get"
 +
* When finished being retrieved, press "Load Genome"
 +
* Note: The length of time it takes to load a genome depends on the load on the database and the number of chromosomes/contigs being loaded.  For this example, it should take a minute or two.
 +
 
 +
===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:
 +
** E. coli annotations: http://de.iplantcollaborative.org/dl/d/C1ACC5C3-1E0B-409B-8A91-C969943F41F8/7122-structural-annotations.gff
 +
** Press "Get"
 +
**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.
  
 
===Comparative Genomics===
 
===Comparative Genomics===

Revision as of 15:58, 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.

Comparative Genomics

Loading your own genome

RNASeq Processing

CoGe Learning Material

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