Revision as of 13:42, 26 August 2016

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.

Selecting

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.

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 in the field to return to 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