How to add a genome from Phytozome or JGI

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Revision as of 15:44, 16 October 2014 by Elyons (Talk | contribs)

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One question we get frequently is how to add data from other genome repositories. This tutorial is for JGI, but should work for most places.

  1. Go to JGI/Phytozome
  2. Go to the download section for your genome of interest
  3. Select and download the assembly (fasta) and annotations (GFF)
    1. Note: Select the gff file that contains both genes and exons "xxx.genes_exons.gff.gz"
    2. Screen Shot 2014-10-16 at 2.16.04 PM.png
    3. Once downloaded, you can send these files to your iPlant Data Store and put them into the coge_data directory (to which CoGe has access), or you can upload them from your desktop. We recommend using the iPlant Data Store due to its more robust file transfer methods. However, your desktop should be fine as long as you have a decent bandwidth.
  4. Log into CoGe
  5. Go to your user profile page
  6. Press "Create" and select "New Genome"
    1. Screen Shot 2014-10-16 at 2.18.56 PM.png
  7. This will take you to LoadGenome (or a popup in your profile for LoadGenome
  8. Fill out the necessary information about the genome.
    1. Note: I like to keep a newly load genome private until I had a chance to make sure the data loaded correctly. Then I make it public.
    2. Note: You can add a link to the data file. Unfortunately, JGI's download is behind an API so a directly link cannot be generated.
    3. Screen Shot 2014-10-16 at 2.27.03 PM.png
  9. Add (upload) the assembly in fasta format.
    1. Screen Shot 2014-10-16 at 2.42.45 PM.png
    2. Screen Shot 2014-10-16 at 2.42.59 PM.png