Visualizing Data

The DNAnexus Platform offers multiple different methods for viewing your files and data.

Previewing Files

DNAnexus supports previewing and opening the following file types directly on the platform:

• TXT

• PNG

• PDF

• HTML

To preview these files, select the file you want 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 in this list, the "Preview" and "Open in New Tab" options appear in the toolbar.

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.

"Preview" opens a fixed-sized box in your current tab to preview the file of interest. "Open in New Tab" enables viewing the file in a separate tab. Due to limitations in web browser technologies, "Preview" and "Open in New Tab" may produce different results.

The file type is not necessarily determined by the file extension. For example, you can preview a FASTA file reads.fa, even though the file extension is not .txt. However, you cannot preview a BAM file (a binary file) using the Preview option.

Preview Restrictions

File preview and viewer functionality are subject to project access controls. When a project has the previewViewerRestricted flag enabled, both preview and viewer capabilities are disabled for all project members. This flag is automatically set to true when downloadRestricted is enabled on a project (for both new projects and when updating existing projects), though project admins can override this behavior by explicitly providing the previewViewerRestricted flag.

Using File Viewers

For file types other than TXT, PNG, PDF, and HTML, the DNAnexus Platform also provides a lightweight framework called Viewers for viewing data with new or existing web-based tools.

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

The data you select to be viewed is accessible by the Viewer, which can also access the Internet. Only run Viewers from trusted sources.

Launching a Viewer

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

This tab opens a window displaying all Viewers available to you within your project. Any Viewers you've created and saved within your current project appear in this list along with the DNAnexus-provided Viewers.

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

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 mapping track you want to visualize, and a pair of *.vcf.gz + *.vcf.gz.tbi for each variant track you want to add. Also, the BioDalliance browser supports bigBed (*.bb) and bigWig (*.bw) tracks.

For more information about BioDalliance, consult BioDalliance's Getting Started. For IGV.js, see the IGV website.

BAM Header Viewer

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

Jupyter Notebook Viewer

The Jupyter notebook viewer displays *.ipynb notebook files, showing notebook images, highlighted code blocks, and markdown blocks as shown in the following example.

Gzipped File Previewer

Use this viewer to decompress a file and inspect its first few kilobytes. The output is similar to what you get from zcat <file> | head. Use this viewer to inspect compressed sequencing files (*.fastq.gz) or compressed variants files (*.vcf.gz). When launching this viewer, select one or more compressed files (*.gz).

Troubleshooting Viewers

If a viewer fails to load, try temporarily disabling browser extensions such as AdBlock and Privacy Badger. Also, viewers are not supported in Incognito browser windows.

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, open a data selector to select inputs for launching a specified Viewer. The Viewer Shortcut includes a Viewer and an array of inputs that are selected by default.

The Viewer Shortcut appears in your project as an object of type "Viewer Shortcut." You can modify the name of the Viewer Shortcut and move it within your folders and projects like any other object in the DNAnexus Platform.