Sending genomes to the iPlant Data Store

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Intro

This tutorial will show you how to send a genome from CoGe to the iPlant Data Store. This is useful for when you want to use a genome outside of CoGe (e.g., in iPlant's Discovery Environment).

CoGe uses iPlant's Authentication and User Identity Management Services for validating users. If you are logged into CoGe, then CoGe can use iPlant's tools and services on your behalf such as retrieving data from and sending data to the iPlant Data Store. In this process, CoGe will add metadata about the genome (organism, original source of the data, etc.)

Log into CoGe

  1. Log into CoGe
  2. If needed: How to get a CoGe account

Find a genome of interest

  1. Use OrganismView to find a genome
  2. When found, click on the link GenomeInfo
  3. Screen Shot 2014-10-01 at 9.36.00 AM.png

Export genome to your iPlant Data Store

  1. To data, find "iPlant Data Store" under tools.
  2. Click "Fasta Sequences" to export the genome's primary sequence
  3. Click "Export GFF" to export the GFF of the structural annotations
  4. Screen Shot 2014-10-01 at 9.39.12 AM.png
  5. Data is exported to a special data in your iPlant Data Store called "coge_data".
    1. Note: CoGe is restricted to only accessing this directory for security purposes.
  6. Screen Shot 2014-10-01 at 9.41.43 AM.png
  7. Screen Shot 2014-10-01 at 9.43.25 AM.png

Find your genome in the iPlant Data Store

  1. Your genome will be exported to the "coge_data" directory in your iPlant Data Store
  2. Screen Shot 2014-10-01 at 9.45.26 AM.png
  3. CoGe will automatically add all its metadata to the genome
  4. Screen Shot 2014-10-01 at 9.46.39 AM.png