EPIC-CoGe Tutorial

Overview

This tutorial is aimed at providing an introductory overview of new features in CoGe for the EPIC-CoGe system. These include:

1. CoGe User accounts
2. Adding private/restricted experiment data (in this case, epigenetic data)
3. Creating Notebooks of collections of data
4. Visualizing experimental data with CoGe's implementation of JBrowse
5. Sharing data with collaborators

Each section has a brief overview of the process and a video on how to do it.

User accounts

The first thing you will want to do is get a CoGe user account. This is very easy:

1. Register an iPlant account
2. Log in

More details on how to get a CoGe account

By having a user account, you will be able to:

• Add private data to CoGe
• Share private data with other users
• Create notebooks (collections of data -- experiments and genomes)
• Have CoGe track your analytical history (makes it easy to revisit old analyses)

Adding private data

"Create" menu on user profile to add new data to CoGe

Once you have a CoGe account, you can add new data to CoGe. To do this:

1. Go to your user profile (click on "My Profile" located in the menu at the top-right of any CoGe page)
2. Click on the "Create" button to get a menu of things you can create

• Select:
  • Load Genome: to load in fasta sequences for a genome
  • Load Annotation: to add genome annotations in GFF to a previously loaded genome
  • Load Experiment: to add quantitative data to an experiment

Example with an Arabidopsis Ago4 mutant

Here we are going to load in an experiment that is based on bisulfite sequencing of Arabidopsis mutants generated by Steven Jacobsen (ref). You can download the data used for this example here.

• Go to your user profile page: (quick link: http://genomevolution.org/CoGe/User.pl)
• Click "Create" located on the left of the page
• Select "Load Experiment". This will link you to LoadExperiment. (quick link: http://genomevolution.org/CoGe/LoadExperiment.pl)
• When LoadExperiment loads, you will have to enter information about the experiment
  • Name: CHH_ago4_Stroud_2013
  • Description: CHH methylation
  • Version: 1
  • Source: Jacobsen Lab
    • Note: First search to see if a data source exists. If it does not, you can create a new one by pressing "new".
  • Restricted: Check!
  • Genome: Arabidopsis thaliana Col-0 (thale cress) (v10.01, id 16911): unmasked
    • An experiment must be linked to a genome. Type in part of the name of an organism to start searching for matching genomes.
• Next comes the part of selecting a data file for the experiment. There are three ways to submit your data file to CoGe:
  • Upload from your computer
  • Fetch from the iPlant Data Store
  • Fetch from a remote http or ftp server