See your data in context with NCBI’s updated Genome Data Viewer

See your data in context with NCBI’s updated Genome Data Viewer

We know it’s important to you to be able to browse and visually inspect variants and alignments from your next-gen sequencing experiments, so we’ve added remote streaming of BAM files to the Genome Data Viewer (GDV). All you need are your BAM files and the index files (.bai extension) in a location that allows HTTP access and you can stream BAM files as custom tracks into the GDV.

GDV add data widget
Figure 1. The GDV add data widget showing the dialog for adding the remote file. To add your data as tracks, use the “Your Data” widget located on the left-side GDV console. Select “Add Remote File” from the supported files menu, click the plus sign  and enter the URL to the file. You can also connect to remote BAM files by using the “Configure tracks” interface available through the “Tracks” button at the upper-right of the sequence viewer display.

After you enter a URL, a progress bar tracks the status of the connection and the validation processes. By default, the file name will be your track’s display name, but you can also enter a custom name for the track. You can easily connect to multiple remote BAM files in this way.

Remote BAM file loaded as track in GDV
Figure 2. GDV showing the remote BAM file loaded as a track. Your files appear as tracks in the graphical display and are listed in the select tracks drop-down menu of the “Your Data” widget, designated by “(R)”. In this case, the track for your BAM data appears at the bottom of the sequence viewer (graphical) panel of the GDV. You can easily re-order the tracks by dragging and dropping individual tracks, or through the “Tracks” button.

Remote data streaming is not supported for other file types or BAM files transferred through FTP or HTTPS.

Try remote streaming today and let us know what you think! If the Genome Data Viewer currently doesn’t support file types you want, use the Support Center to tell us – or send us an email. For more information on how to use this new feature, please see the GDV Help documentation.

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