User-defined Data

This page outlines how to prepare data for use with IGV for iPad.

  1. Create a file in one of the supported formats described below.
  2. Make the file accessible via a web URL. The file can be hosted anywhere on the web, or on your local intranet. The mechanism used for making a file web-accessible is independent of IGV, and detailed documentation of the many options for sharing data on the web is beyond the scope of this user guide. However, below we provide instructions for some easy-to-use options. Your IT department may have other suggestions, or may help you install your file on a local web server. 

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:

Sharing Data Files on the Web

You can make your data files web-accessible by taking advantage of data hosting services, or other environments that allow you to store and access cloud data. Each of the websites mentioned below has more detailed help information. Another option is to contact your IT department for help installing your files on a local web server.

Use GenomeSpace, a freely-available environment for integrative genomics analysis. First, you will need to sign up for an account on the GenomeSpace website.

  1. On your desktop computer (not on your iPad), log in to your account on the GenomeSpace site.
  2. Upload a file to your GenomeSpace account:
    1. Drag a file from your desktop and drop it onto one of your GenomeSpace folders.
  3. Make your file publicly available:
    1. Select the uploaded file by clicking on the checkbox next to its name.
    2. Click on the File menu, and select Sharing
    3. A new window will appear. Click on the Edit Sharing button.
    4. Check the box labeled Allow public access, and click on the Grant Permissions button.
  4. Get the web address of the file in GenomeSpace:
    1. Select the shared file by clicking on the checkbox next to its name.
    2. Select View Link URL from the File menu.
    3. Copy the link, and save it for use with IGV for iPad.

Use Simple Storage Service (S3), a data-hosting service offered by Amazon Web Services (AWS). First, you will need to sign up for an account on the AWS website

  1. Log in to your account using the AWS Management Console. Amazon also has a mobile version of the console in the Apple App Store.
  2. Upload a file to a bucket in your S3 storage:
    1. Click on a bucket in your AWS account, or first create a new bucket by clicking on the Create Bucket button. A new window will appear. Enter the bucket name and click the Create button.
    2. In your bucket, click on the Actions menu, and select Upload.
    3. A new window will appear. Click on the Add Files button.
    4. Select a file on your computer that you would like to upload to S3.
    5. Click the Start Upload button.
  3. Make your file publicly available:
    1. Click to select the uploaded file in your bucket.
    2. Click on the Actions menu, and select Make Public.
  4. Get the web address of the file in S3:
    1. Click to select the shared file.
    2. Click on the Properties button and copy the contents of the Link field. Save the URL for use with IGV for iPad.

Use Dropbox, a popular commercial web-based data-hosting service. First, you will need to sign up for an account on the Dropbox website

  1. Log in to your account on the Dropbox site.
  2. Upload a file to your Public folder in Dropbox: (Note: Dropbox Basic accounts no longer have Public folders.)
    1. Click the Public folder to open it.
    2. Click the Upload icon at the top of the window.  
    3. A new window will appear. Click the Choose File button.
    4. Select one or more file on your computer that you would like to upload to Dropbox.
    5. Click the Start Upload button.
  3. Get the web address of the file in Dropbox:
    1. Right-click (command-click on the Mac) on the uploaded file in the Public folder to bring up a popup menu.
    2. Select Copy public link from the menu, and save the URL for use with IGV for iPad.

Once you have the URL link to your file, you can load it into IGV for iPad by tapping on Tracks > My Track and typing or pasting the URL into the dialog that pops up. See Manage Data Tracks for more details.

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.