Loading IGV data from Albiorix - The-Bioinformatics-Group/Albiorix GitHub Wiki

While IGV isn't currently installed on Albiorix, it is possible to load data stored there into your local copy of IGV.

1. Open IGV, and open the Preferences menu under View > Preferences.

2. In the Advanced tab, adjust the Genome Server URL and Data Registry URL:

   • Genome Server URL: http://albiorix.bioenv.gu.se/igv/genomes.txt
   • Data Registry URL: http://albiorix.bioenv.gu.se/igv/igv_registry.txt

3. Restart IGV. You will be asked to authenticate (the username and password can be provided on request).

4. To load a genome, open Genomes > Load Genome From Server, and select the desired genome.

   • Hovering over a gene model in the Gene track will display a tooltip, which will show the gene name (currently from a quick and dirty annotation), in addition to the gene ID which is displayed by default

5. To load data tracks, open File > Load From Server, tick the desired data, and click OK

   • Note that depending on your hardware, loading too many tracks at once may result in 'Out of Memory' errors, and may be hard to view on smaller displays.
   • To get around this, I recommend loading a few tracks (5-10 bam files) at a time, and saving each subset of files as a session (File > Save Session), allowing you to quickly load up and view smaller batches of files.