EPIC CoGe Reference

EPIC-CoGe is a custom version of JBrowse with a lot of added features and functionality. The data tracks are populated dynamically from CoGe.

Track Selector

The Track Selector lists your CoGe experiments and notebooks as well as public experiments and notebooks associated with the genome you are viewing.

When you mouse over an item in the Track Selector, a popup menu appears to the right of the item. The popup is used for managing data in CoGe. See Managing Experiments and Managing Notebooks below.

Viewing Tracks

Click on a track to view it in the browser. Click on it again to remove it from the browser. When viewing tracks they are assigned a color in the browser and the corresponding item in the Track Selector is highlighted in the same color.

When you view a notebook track, all the experiments in the notebook are shown together in a single track. Each experiment in the notebook is assigned a different color in the browser and a circle of the same color is shown in the Track Selector for that experiment. The notebook track in the Track Selector is highlighted in grey.

Tracks that are being viewed in the browser have a label on the left with a popup menu.

The menu is used for temporarily transforming track data, searching the track data, and saving search results as a new experiment (see below).

Track Metadata

When you mouse over an item in the Track Selector, a metadata tooltip pops up to the side.

Filtering

Type text in the field at the top of the Track Selector to narrow the list to tracks whose names, descriptions or metadata match the text.

Click the X the appears in the field to clear the filter and display the full list.

You can also filter the list by data type. Click on the popup menu to the right of the field and select one of the Show ... Tracks items. For example, selecting Show Quantitative Tracks will narrow the list to only show experiment tracks with quantitative data.

Select Add All Tracks Shown from the popup menu to add all the currently shown tracks to the browser.

Select Clear All Tracks to empty the browser.

Feature Search

Click on the Find Features button on the main toolbar.

In the window that pops up, enter the partial text of the feature name you want to search for.

Use the chromosome popup to search only on a particular chromosome or on any.

Check one or more feature types to search and then click OK.

The matching features are display in a list next to the Track Selector.

Click on a feature to jump the browser view to that feature.

Search Tracks

Searching of track data is done via the popup menu on the label of the track when it is being viewed in the browser. The types of searches vary by the type of data.

Quantitative Tracks

Use the chromosome popup to indicate whether you want to find data on a particular chromosome or on any.

Choose between finding the maximum values, the minimum values or a range of values.

To enter a range of values to find, click and drag on the histogram or enter values in the fields.

Track Overlaps

There are three different types of track overlaps that you can compute by dragging one track onto another. To perform one of the overlap computations:

• click and drag on the first track
• move the mouse over the second track
• hold the Command/Ctrl key down while still holding the mouse button down. If you move around while holding the Command/Ctrl key, the little arrow icon should change to a plus icon.
• release the mouse button to drop the first track onto the second one. A dialog window will appear where you can choose which type of computation to perform.

Types

1. Find data in the first track that overlaps data in the second track. This creates a new search track with only the overlapping data from the first track.
2. Find data in the first track that does not overlap data in the second track. This creates a new search track with only the non-overlapping data from the first track.
3. Merge tracks. This creates a new merge track with all the data from both the first and second tracks. You can then drag and drop additional tracks onto the merge track. Using the label menu for the merge track you can create a new notebook in CoGe (if you are logged in to CoGe) that contains the experiments represented by the tracks that have been merged.

Create New Experiment from Search Tracks

Search results may be saved to CoGe as a new experiment.

Select Save Results as New Experiment from the label popup menu for the track.

Managing Experiments

Experiment View

Select "Experiment View" from the track's popup menu in the Track List, or the track's label popup menu in the track browser to open CoGe's ExperimentView window for the experiment.

Renaming Experiments

1. Select "Rename" from the track's popup menu in the Track List
2. Enter the new name in the dialog window that appears
3. Click the OK button.

Note: the experiment may move after it is renamed because notebook contents are kept sorted.

Adding Experiments to Notebooks

There are two ways to add an experiment to a notebook:

1. Drag the experiment track in the Track List and drop it on the notebook track in the Track List. Note: the experiment may be moved after you drop it because notebooks are kept sorted.
2. 1. Select "Add to Notebook" from the experiment track's popup menu in the Track List
   2. select the notebook you want in the dialog that appears
   3. click OK

Removing Experiments from Notebooks

1. Select "Remove from Notebook" from the track's popup menu in the Track List
2. Click the OK button.

The experiment is removed from the notebook but may still be found in other Notebooks it belonged to and in All Experiments.

Deleting Experiments

1. Select "Delete" from the track's popup menu in the Track List
2. Click the OK button.

Note: Deleting an experiment will move it to the trash.

Managing Notebooks

Notebook View

Select "Notebook View" from the track's popup menu in the Track List, or the track's label popup menu in the track browser to open CoGe's NotebookView window for the notebook.

Renaming Notebooks

1. Select "Rename" from the track's popup menu in the Track List
2. Enter the new name in the dialog window that appears
3. Click the OK button.

Note: the notebook may move after it is renamed because the list of notebooks is kept sorted.

Deleting Notebooks

1. Select "Delete" from the track's popup menu in the Track List
2. Click the OK button.

Note: Deleting a notebook will move it to the trash. Experiments in the notebook will NOT be deleted.

Settings

To set whether the Track Selector is shown on the right or the left side of the window, select Move Track Selector to Left(Right) Side from the popup menu at the top of the Track Selector.