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Hey Enrique,
To answer your question from a Unix perspective: GenomeBrowse will see the file system like any other application and symbolic links are handled by the OS to look like the files they soft link to.
As long as the .bam and .bam.bai file are still side-by-side it shouldn't matter if they are being read through a symbolic link.
In fact, I use this quite a lot when testing etc.
Thanks, Gabe
