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.
DNAnexus allows users to preview and open the following file types directly on
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
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.
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
option. To view BAM files on the platform, see the
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
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
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).
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 would like to visualize, and a pair of
*.vcf.gz.tbi for each
variant track you want to add. In addition, the BioDalliance browser supports
*.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 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
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 (
create custom viewers to
visualize data on the platform.
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