How to load a private genome into CoGe?

Disclaimer

To perform the advanced genomic analyses with CoGe, you need to have your genome added to the system. We are working to make this entire process automated so that any user can add a genome without needing to contact anyone in the CoGe project, but currently the genomes must be added by hand. We prefer to use iPlant's Data Store to transfer your personal data to CoGe because the Data Store is relatively easy to use (like dropbox), has a lot of free storage for scientists, and is very fast. Until the upload to CoGe has been automated, a project member will add your data to the CoGe system while keeping it accesible only to you. Keep in mind that, once generated, the Data Store web link can be used by anyone who has the URL. For this reason, please un-share or delete the file as soon as you receive notification from the CoGe project that your data has been received.

Loading Fasta Files from the Web:

You can now load in fasta files from within CoGe:

1. Log into CoGe
2. Go to your User Profile Page
3. Select "Create" -> "Load Genome"

Note: You will still need to send us your GFF file to add gene models and annotations. This is because every GFF file is different and we still need to validate the transformation of your data into CoGe's internal data model for gene annotations. If you would like us to add annotations to your genome, please send us a link to download the GFF file as well as the genome id of the genome to which they will be associated.

Quick Guide

(These directions should also be followed for public genomes.)

1. Register your CoGe account:
   1. How to get a CoGe account
2. Upload Fasta and GFF (if available) files to iPlant Data Store
   1. Quick Start Guide: https://pods.iplantcollaborative.org/wiki/display/start/Data+Store+Quick+Start
   2. Use Davis to generate a quick-share link to let others download the data
3. Email the CoGe Team ([1]) the following information
   1. Real Name
   2. iPlant user name
   3. Quick-share links to genome data files
   4. Organism name
      1. Aquilegia coerulea (columbine)
   5. Organism NCBI taxonomic description
      1. Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliophyta;eudicotyledons;stem eudicotyledons;Ranunculales;Ranunculaceae;Aquilegia;
      2. Search: http://www.ncbi.nlm.nih.gov/taxonomy
   6. Name of data source:
      1. JCVI
      2. Dr. Lyons Lab
   7. Description of data source:
      1. J Craig Venture Institute
      2. University of Arizona
   8. Link to the data source
      1. http://www.jcvi.org/
   9. Version of genome
   10. Type of genomic sequence:
       1. unmasked
       2. masked
       3. Current list in CoGe: http://genomevolution.org/CoGe/SeqType.pl
   11. Link to information about the genome
   12. Is the genome "public" or "restricted"