Visualizing Data

There are several different methods with which you can view your files and data on the DNAnexus platform.

To learn how to use IGV on your local machine, please see Using IGV with DNAnexus.

Previewing Files

DNAnexus allows users to preview and open the following file types directly on the platform:

  • TXT
  • PNG
  • PDF
  • HTML

To preview these files, select the file you wish to view by either clicking on its name in the Manage tab or selecting the checkbox next to the file. If the file is one of the file types listed above, you will see the Preview and Open in New Tab options in the toolbar above (see (1) in the screenshot below).

Alternatively, you can click on the three dots on the far right and choose the Preview or Open in New Tab options from the dropdown menu (2).

Preview will open a fixed-sized box in your current tab for you to preview the file of interest. Open in New Tab will allow you to view the file in a separate tab. Due to limitations in web browser technologies, Preview and Open in New Tab may yield different results.

Previewing files on the DNAnexus platform.

NOTE: The file type is not necessarily determined by the file extension. For example, you will be able to preview a FASTA file `reads.fa`, even though the file extension is not `.txt`. However, you will not be able to preview a BAM file (a binary file) using the Preview option. To view BAM files on the platform, see the Viewers section below.

Using File Viewers

For files not listed in the section above, the DNAnexus platform also provides a lightweight framework called Viewers, which allows users to view their data using new or existing web-based tools.

A Viewer is simply an HTML file that you can give one or more DNAnexus URLs representing files to be viewed. Viewers generally integrate third-party technologies, such as HTML-based genome browsers.

NOTE: The data you select to be viewed will be accessible by the Viewer, which can also access the Internet. You should only run Viewers from trusted sources.

How to launch a viewer

You can easily launch a viewer by clicking on the Visualize tab within a project.

A project's Visualize tab.

This tab will open a window showing all Viewers available to you within your project. If you have created any Viewers yourself and saved them within your current project, these will show up in this list along with the DNAnexus-provided Viewers.

Clicking on a Viewer will open a data selector for you to choose the files you wish to visualize. Tick one or more files that you want to provide to the Viewer. (The Viewer does not have access to any other of your data.) From there, you can either create a Viewer Shortcut (see (1) in the screenshot below) or launch the Viewer (2).

List of DNAnexus viewers.

Example Viewers

Human genome browsers (BioDalliance, IGV.js)

The BioDalliance and IGV.js viewers provide HTML-based human genome browsers which you can use to visualize mappings and variants. When launching either one of these viewers, tick a pair of *.bam + *.bai files for each mappings track you would like to visualize, and a pair of *.vcf.gz + *.vcf.gz.tbi for each variant track you want to add. In addition, the BioDalliance browser supports bigBed (*.bb) and bigWig (*.bw) tracks.

For more information about BioDalliance please consult this page http://www.biodalliance.org/started.html. For IGV.js please see http://igv.org/web/doc/.

BAM header viewer

The BAM Header Viewer allows you to peek inside a BAM header, similar to what you would get if you were to run samtools view -H on the BAM file. (BAM headers include information about the reference genome sequences, read groups, and programs used). When launching this viewer, tick one or more BAM files (*.bam).

Gzipped file viewers

This viewer allows you to uncompress and see the first few kilobytes of a gzipped file. It is conceptually similar to what you would get if you were to run zcat <file> | head. Use this viewer to peek inside compressed reads files (*.fastq.gz) or compressed variants files (*.vcf.gz). When launching this viewer, tick one or more gzipped files (*.gz).

Custom Viewers

Developers comfortable with HTML and JavaScript can create custom viewers to visualize data on the platform.

Viewer Shortcuts

Viewer Shortcuts are objects which, when opened, will open a data selector to select inputs for launching a specified Viewer. The Viewer Shortcut includes a Viewer and an array of inputs that will be selected by default.

The Viewer Shortcut will show up in your project as an object of type "Viewer Shortcut." You can change the name of the Viewer Shortcut and move it within your folders and projects as you would any other object in the DNAnexus platform.

A viewer shortcut.

Last edited by Maria Nattestad, 2017-09-12 21:58:59

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