User-defined Genomes

IGV for iPad provides the reference genomes described in Hosted Genomes & Public Data Tracks. You can also use another reference genome, provided the sequence file is web-accessible.

  • Options include installing the file on your own web server.
  • Or take advantage of a data-hosting service such as Dropbox.

Igvtools functions are provided in the Tools menu of desktop IGV.

Prepare Genome Files

The following files define a reference genome in IGV for iPad.

  • Required are the genome sequence in FASTA format and an accompanying index file.
  • Optional is a cytoband file in the format used by desktop IGV to display an ideogram of the chromosome cytobands.
  • Optional are genome annotations in BED format and an accompanying index file. If provided, these load automatically when the genome is selected.
    • Create the index file using either the index command of igvtools or tabix SAMtools.
    • You can create a BED file containing only your genomic regions of interest, much like a selective Genes track, using desktop IGV. Define your regions of interest, including names for the regions, by following the directions here. Then go to the menu, select Regions>Export Regions and save the BED file. This in turn is used to create the index file.

The paired files, the FASTA file and its index or the BED file and its index, must be in the same folder.

Manage New Genome

Add a user-defined genome to the menu. Note the new genome is not automatically selected when it is added to the menu.

  1. Tap on the Genomes button in the toolbar, and tap on Add Genome.
  2. Enter the following in the dialog box that appears and tap Save.
    • The name of the genome for the Genomes menu
    • The HTTP web addresses for the genome sequence file, the cytoband file, and the annotation file

Select the user-defined genome from the same menu as the hosted genomes.

  1. Tap the Genomes button.
  2. Select the genome and then the chromosome.

Remove a user-defined genome from the menu.

  1. Tap the Genomes button and tap Edit.
  2. From the menu, tap the red circled bar to the left of the genome entry.
  3. Tap the Delete button that appears on the right and tap Done