Manage Data Tracks

This page provides instructions on loading other data tracks and managing displayed tracks.

My Tracks

The Public Tracks menu provides convenient access to a number of publicly available datasets, as described in Hosted Genomes & Public Data Tracks. You can also load any dataset for viewing in IGV for iPad, provided you have the HTTP web address and its format is supported by the app (see supported File Formats). Given the iPad's limited memory resources, a file that is easily supported by desktop IGV may take longer to load on IGV for iPad.

Add a new track

  1. Tap on the Tracks button in the toolbar and select My Tracks.
  2. Tap Add Track. In the dialog box that appears, type or paste the HTTP web address of the file, and optionally enter a track label. Tap Done.
  3. The new track displays as the topmost track. 

The new track is also added to the My Tracks menu for the corresponding genome. The menu does not allow tracks with duplicate web addresses and they will be ignored.

Reload a track that was previously added.

  1. Make sure the current genome corresponds to the saved track.
  2. Tap the Tracks button and select My Tracks
  3. In the scrollable menu, find and select the track of interest. Both the label and the web address are listed for each entry.

Delete a track from the menu.

  1. Tap the Tracks button and select My Tracks.
  2. Tap Edit and from the menu, tap the red circled bar to the left of the track entry.
  3. Tap the Delete button that appears to the right and tap Done.

Track Control Menu

Press and hold on a displayed track to pop up a menu. Depending on the type of track, additional menu choices become available. Menu choices are applied to All Tracks or to the selected track under This Track. Certain adjustments for specific tracks do not save to sessions.

        

  • All Tracks
    • Hide or Show Track Labels on the upper left corner of each track.
    • Reorder Tracks by holding and dragging items via the triple-bar symbol to the desired order. Tap Done to update the display.
  • This Track. The menu tail points to the selected track.
    • Delete Track is in red. Tap to remove the track from display.
      • Alternatively, find the item under the Tracks menu and toggle the slider to the grey position to remove it from display.
    • Rename Track provides a textbox to input a new track name.
    • Set Data Range allows you to define the minimum and maximum vertical signal range to display for bar chart tracks. Alternatively, set the Auto Scale blue toggle switch for automatic scaling.
      • IGV for iPad automatically resets the signal display range based on the track's dynamically loaded data values. Thus, with Auto Scale on, changing the view will readjust the displayed range.  
    • A Squish and Expand toggle adjusts the vertical height of displayed components of a sequence alignment track or a segmented copy number track.
    • Sort reorders displayed components of a sequence alignment track or a segmented copy number track.
      • Sequence alignments reorder by nucleotide at the locus you pressed that popped up the menu. Nearby putative SNPs highlighted by a colored bar in the coverage track will define the sort locus. Otherwise, the sort is performed on the region central to the finger press.
      • Copy number data reorders by copy number values in the region defined by the width of the finger press. Multiple sorts will toggle between sorting by amplification and deletion.

Track Preferences

To help manage memory resources for sequence alignment data, IGV for iPad provides app-specific adjustable preferences under iPad Settings

  • Alignment Visibility Threshold sets the maximum display region size for sequence alignments to be retrieved from the file and displayed. Views zoomed out to larger regions will display a message to zoom in to see the alignments.
    • The default value is 4 kb.
  • Downsampling Window Size and Window Depth control the random sampling method used to reduce the number of reads stored in memory and displayed.
    • The default values are 50 bases (width) and 30 (depth).