just download the IGV binary distribution from the Broad's website, unpack and 
start the appropriate file (it depends on your OS, explained in the readme). 
Then. in Galaxy, open the BAM file by clicking on "display with IGV LOCAL". 
Each BAM file will be loaded into the same window of IGV.

Alternatively, download the BAMs, open the IGV and load files locally from your 


Helmholtz Zentrum München
LMU München
mail: sebastian.vosb...@helmholtz-muenchen.de
From: galaxy-user-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Ben Gift 
Sent: Wednesday, September 25, 2013 11:02 PM
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Trying to visualize 2 bam files from Galaxy

I'm trying to start a visualizer with two different files to show a person 
where the variants are. Can I start IGV or something like it with multiple 
files? I read the docs and didn't find anything about it. I also asked here 

Helmholtz Zentrum München
Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
Ingolstädter Landstr. 1
85764 Neuherberg
Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe
Geschäftsführer: Prof. Dr. Günther Wess Dr. Nikolaus Blum Dr. Alfons Enhsen
Registergericht: Amtsgericht München HRB 6466
USt-IdNr: DE 129521671

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