Difference between revisions of "Genome viewer"

• Add data
• Move the genome position, zoom in, zoom out
• Manage displayed datasets

Omics data viewer

The panel in which "omics" datasets are displayed

Genome annotation

All genome features available for the displayed Listeria strain genome.

Mouse interactions

• Left-click on the omics data viewer will display a vertical line indicating the genome position in base pair (bp).
• Left-click on the genome annotation panel will display more information on the selected genome feature.
• Right-click on the genome annotation panel will center the view.
• Double-click on the genome annotation panel will open the corresponding gene or small RNA webpage.

Two buttons are available to add datasets, one for transcriptomic data, the other for proteomic. Both will open a similar dialog with all datasets available. The user can filter datasets or directly search them. Every dataset selected will be displayed on the genome viewer by clicking on the Ok button.

• Scroll the genome by searching a specific element contained in the displayed Listeria strain genome.
• Zoom in and zoom out horizontally, to change the base pair scale of display.
• AT button gives instant access to a view at the sequence scale where DNA sequence is displayed, along with amino acid sequence in the 6 possible frames.
• Increase the height of all genome tracks.

There are 4 different buttons in this panel:

• Access the dialog window to look at the data legend and remove specific datasets from the view
• Save in text file the current genome viewer properties
• Change the display between absolute expression value (Log(expression)) to relative expression value (Log(Fold Change)). Thus, the user can switch from displaying biological condition absolute expression datasets to comparisons of biological conditions relative datasets.
• Select one of the three representation types: Display by biological condition, by dataset, or overlap all datasets on one single track.

• RNASeq data
• Tiling array
• Gene expression array
• Transcription Start Site (TSS) data
• Proteomic data:

For each track the name of the dataset displayed is shown on the top left. The grey line in the middle of each track is the value 0. If the name of the dataset contains "vs" it means it is a relative expression dataset, thus Log(Fold Change) values are displayed. The type of data displayed is written at the end of each dataset name on the top left of each track.

• Move view vertically:

When the height of the view has been increased or decrease using the Height zoom the vertical slider will be used to move from one dataset to the other.

• Base pair position: Show the position in base pair (bp) in the Listeria strain genome displayed.
• Genome annotation: All the genome features available are displayed here. With a fix color code.
• Move view horizontally: To move horizontally the genome viewer and browse the genome.