There are several different methods to view your files and data on the DNAnexus
DNAnexus allows users to preview and open the following types of files directly
on the platform:
To preview these files, select the file you wish to view by either clicking on
its name in the Manage tab, or selecting the box 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 menu above (see (1) in the screenshot below).
Alternatively you can right-click on the file 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, previewing a file may
occasionally look different (more limited) than opening in a new tab.
: 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
view BAM files on the platform, see the 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 which is given one or more DNAnexus URLs
representing files to be viewed. Viewers have been most commonly used to
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
This tab will open a window showing all the possible 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
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 launch the Viewer (See (2) in the screenshot below), or create a
Viewer Shortcut (1).
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
*.bai files for each mappings track
you want visualized, and a pair of
*.vcf.gz.tbi for each variants
track you want to add. In addition, the BioDalliance browser supports bigBed
*.bb) and bigWig (
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
Gzipped File Previewer
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
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 (
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. In the case of
the above screenshot, all the selected files will be opened by the Viewer.
The Viewer Shortcut will show up in your project as an object of type "Viewer
Shortcut." Hovering over the tag icon next to the name of the object will allow
you to see which files have been configured to be selected by default by this
shortcut (see screenshot below). Additionally, you can also 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.