How to add a genome from Phytozome or JGI
Revision as of 16:57, 16 October 2014 by Elyons
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.
- Go to JGI/Phytozome
- Go to the download section for your genome of interest
- Select and download the assembly (fasta) and annotations (GFF)
- Note: Select the gff file that contains both genes and exons "xxx.genes_exons.gff.gz"
- 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.
- Log into CoGe
- Go to your user profile page
- Press "Create" and select "New Genome"
- This will take you to LoadGenome (or a popup in your profile for LoadGenome
- Fill out the necessary information about the genome.
- 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.
- 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.
- Add (upload) the assembly in fasta format.
- Press the red "Load Genome" button located at the bottom of the data selections
- A popup will appear stating that your genome is being loaded
- When the genome has been loaded successfully, you'll get a thumbs-up and a link to go to GenomeInfo
- GenomeInfo will appear in a popup in your profile page or in a new window. GenomeInfo lets you get detailed information about your genome, manage data about the genome, send it to CoGe's analysis tools, and associate new data to the genome.
- To add structural annotations to your genome, press "Load Gene Annotations"
- This will popup (or a load new window) of LoadExperiment.
- LoadExperiment will ask you to add information about your genome and to upload a GFF file for the annotations.
- Add information about the annotation file and add your GFF file
- Note: the gff file can be compressed in gzip
- Press the red "Load Annotation" button to start loading the annotations
- Note: Loading these annotations may take a while