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

You can find where to log into CoGe at the top of every page. Also, there is a handy link for getting a CoGe account.

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

Adding an epigenetics experiment to the genome of Arabidopsis thaliana

Additional annotations added for an experiment to provide provenance and detailed metadata.

Experiment highlighted in user profile where it can be easily shared with other users

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

• After the experiment has been added, you can manage its information in ExperimentView:
  • Change its name, description, source and version
  • Add experiment types to it (e.g. BS-Seq)
  • Make it public or private
  • Add annotations: these are additional descriptors (text, images, and links) for the experiment
• The experiment now shows up in your user profile
  • Note: If the experiment was marked as being restricted, a "®" shows up next to its name

Creating Notebooks to manage collections of data

Popup box to fill out when you create a notebook in the user profile page.

Showing the newly created notebook entitled "Arabidopsis Ago mutants". By hovering the mouse over the notebook, information about the notebook appears to the right of the "my stuff" list.

Notebook containing multiple experiments. Note that of the experiments, one is private and several are public.

CoGe's Notebooks are designed to make it easy to organize a set of data (genomes, experiments, genomic features) and add additional information/metadata in the form of annotations to the collection of data. In addition, notebooks can be shared with other users of CoGe and are also used to bundle data together in various tools. For example, the EPIC-CoGe Browser uses notebooks to display multiple experiments in the same track.

To create a notebook

• Go to your user profile page. (quick link: http://genomevolution.org/CoGe/User.pl)
• Click the "Create" button located on the right side of the page and select "New Notebook".
• A box will appear titled "Create New Notebook". Here, type in a name, description (optional), and select the type.
  • Type is to help you organize your data.
• Click the red "Create Notebook" to create the notebook.
• The notebook will now in the list of your items. You can search for it by name using the text box located at the top right of the list, or only show notebooks by click on the notebook icon.
  • If you hover over the notebook, information about the notebook appears to the right of the "my stuff" list.
• To add information to the notebook, click on the notebook which will take you to NotebookView. (quick link: http://genomevolution.org/CoGe/NotebookView.pl?nid=503)
• In NotebookView, click "Add Items" to add items:
• When the "Add Items to Notebook" popup box appears, you can select the types of data to search and then use the textbox to type in a search tearm.
  • The different tabs limit which sets of data to search -- my stuff are things you have added or have been given access, the others are for public data
• Find the experiment you previously added to CoGe. In this example, the experiment was named "ago4_mutant". Once you find it, select it and press the "Add Selected Items" button.
• Next, search for additional "Ago" mutants by search through the public experiments and add them to your notebook.
• Next, add an annotation to the notebook by pressing the "Add Annotation" button and filling out the popup box.
  • In the example shown, the annotation included a figure from a Plant Physiology article on gene silencing movement in Arabidopsis.

To visualize experiments in the [EPIC-CoGe Browser]]

View of the EPIC-CoGe Browser showing various tracks. Of interest are the tracks showing different types of quantitative data from experiments, including tracks that have multiple experiments. To the left of the viewer is the menu for finding and selecting tracks for visualization. If you mouse over quantitative data, colored values appear that correspond to the various experiments. Note that the track with multiple experiments is organized as a Notebook.