Difference between revisions of "EPIC-CoGe Tutorial"

From CoGepedia
Jump to: navigation, search
(User accounts)
(Adding private data)
Line 68: Line 68:
 
* The experiment now shows up in your [[user profile]]
 
* 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
 
**Note: If the experiment was marked as being restricted, a "®" shows up next to its name
 +
 +
== Creating [[Notebooks]] to manage collections of data ==
 +
[[File:Screen Shot 2013-05-30 at 11.19.08 AM.png|thumb|600px|right|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]]. ]]
 +
 +
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.

Revision as of 11:26, 30 May 2013

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

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

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.

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.