Hi, I am Crystal. 
I tried to visualize Tophat output (BAM and BED files) together with UCSC 
Zebrafish refgene track chr21.bam (downloaded from  
http://genome.ucsc.edu/cgi-bin/hgTables) using Visualization in Galaxy Test but 
nothing appeared.
The workflow I did was:
1) selecting Visualization > New Track Browser
2) In New Track Browser, I select Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7) 
for Reference genome build (dbkey)
3) Click continue
4) Option > Add tracks
5) Select 3 datasets (BAM, BED from tophat output and refgene track file)  >  
6) Select chromosome 21
Nothing can be seen.
Jeremy, can I get advice on this? 
Best regards,
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