This tutorial is aimed at providing an introductory overview of new features in CoGe for the EPIC-CoGe system. These include:
- CoGe User accounts
- Adding private/restricted experiment data (in this case, epigenetic data)
- Creating Notebooks of collections of data
- Visualizing experimental data with CoGe's implementation of JBrowse
- Sharing data with collaborators
Each section has a brief overview of the process and a video on how to do it.
The first thing you will want to do is get a CoGe user account. This is very easy:
- Register an iPlant account
- Log in
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
Once you have a CoGe account, you can add new data to CoGe. To do this:
- Go to your user profile (click on "My Profile" located in the menu at the top-right of any CoGe page)
- Click on the "Create" button to get a menu of things you can create
Example with an Arabidopsis Ago4 mutant
- 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
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