User-defined Data

This page outlines how to prepare data for use with IGV for iPad, including links to descriptions of the supported file types. Instructions on loading the prepared files onto IGV for iPad are in Manage Data Tracks.

Prepare Data Files

Follow these two steps to prepare IGV for iPad compatible data files.

  1. Create a file in one of the supported formats described below.
  2. Make the file web-accessible to the iPad device.
    • Options include installing the file on your own web server
    • Or take advantage of a data-hosting service such as Dropbox.

IGV for iPad supports HTTP Basic Authentication and will prompt you for a username and password if the file has been protected. At this time, authentication is not supported for BAM files.

Data Types and File Formats

The file name must indicate the file type using the 3-letter extension. IGV also supports gzip compressed files with a .GZ extension appended to the file name. IGV for iPad supports the following data types and formats.

  • Genomic features and annotations in BED format.
    • Indexed BED files are also supported and must reside in the same directory as the corresponding BED file.
  • Sequence alignments in BAM format.
    • The BAM alignment file must be coordinate sorted and have a corresponding index file, with BAI extension. Place both files in the same directory.
      • The GenePattern module Picard.SortSam will sort and index BAM files.
        • Select coordinate sort order and BAM output format to produce IGV-compatible sorted BAM file and BAI index file.
    • The related SAM format is not supported by IGV for iPad.
  • Segmented copy number data in SEG format.
  • Numeric data in WIG format.
  • Numeric data in BIGWIG format.
  • Numeric data in TDF format.
    • Currently, only single-track TDF files are supported.

Given the iPad's limited memory capacity, IGV for iPad cannot support the same magnitude of data as desktop IGV. 

  • Avoid using large files.
  • To increase efficiency of data loading: