Layout, Toolbar, & Navigation

This page provides a basic overview of the IGV for iPad screen layout, the functions provided by the toolbar, and how to navigate the view.

Screen Layout

  1. The toolbar at the top of the screen provides access to commonly used functions and is described in the next section.
  2. Below the toolbar, an ideogram displays the cytobands of the current chromosome.

  3. The red box on the chromosome ideogram indicates the portion of the chromosome displayed. When zoomed out to the full chromosome, the red box disappears.

  4. The space below the chromosome is reserved for displaying nucleotide sequences, either in coded color bars or actual sequence when the view is sufficiently zoomed in, as shown in the next image. Color bars appear at ~5 kb zoom level, with A=green, T=red, G=yellow, C=blue, and N=black.

  5. The remaining area of the screen is devoted to horizontal tracks that display data and annotations. Hosted reference genomes will automatically load the Genes annotation track.

Toolbar

The toolbar at the top of the screen provides the main controls for the app.

  1. Tap on Genomes for a menu to select the reference genome and the chromosome to display.  One chromosome can be displayed at a time.
  1. Tap on Tracks to display a menu to load data, either Public Tracks or user-defined My Tracks.
  1. Tap on Sessions to display a menu to save, load, or edit bookmarked sessions. Saved sessions recall the genome, tracks, locus view, and zoom level.
  1. The text box displays the currently viewed locus. You can also enter a locus or the name of a gene to view. Gene names must follow HUGO Gene Nomenclature, e.g. TP53 and not P53. 
  1. The slider controls the zoom level. You can also zoom in and out by using the normal iPad controls of pinching and double tapping as detailed in the next section.

Navigating the View

The initial view will be of the whole chromosome. Use the following controls and gestures to navigate the view. 

  • Zoom functions are summarized in the table. Note tapping zooms by factors of four.
Zoom Pinch Tap Slider Text box
 More detail Pinch open 1-Finger double tap Right Enter nucleotide range using format [chromosome]:[start base]-[end base], e.g. chr5:90,339,000-90,349,000
 Less detail Pinch close 2-Finger single tap Left
  • Pan. Swipe the tracks to pan across genomic coordinates. Alternatively, tapping on the chromosome ideogram will move the view to that locus, maintaining the same zoom level.
  • View region by locus. Use the text box as described in the table to view a specific region by base pair range.
  • View region by gene. To view the locus of a gene, enter the gene symbol in the text box. Gene names must follow HUGO Gene Nomenclature, e.g. TP53 and not P53.
  • Load a saved session. Tap on the Sessions button to bring up a list of saved sessions, and then select an entry in the list. For instructions on saving and managing sessions, go to Manage Sessions.