IGV should allow you to do this  but not sure about trackbrowser in Galaxy.

--- On Wed, 8/3/11, Jiannong Xu <jxu@nmsu.edu> wrote:

From: Jiannong Xu <jxu@nmsu.edu>
Subject: [galaxy-user] visualization
To: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Date: Wednesday, August 3, 2011, 6:03 PM

Hi Jen,

I mapped illumine reads to draft genomic contigs, and try to visualize the mapping. Is there any way I can use my own reference contigs for visualization?


John Xu

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