Austin,

See this discussion for ideas about how to generate partial and full coverage 
data from a Tophat BAM file:

http://gmod.827538.n3.nabble.com/get-wig-file-after-tophat-td2547963.html#a2548359

Short answer: use the pileup tool for partial coverage (i.e. coverage for all 
bases that have mapped reads) and use other tricks to generate coverage data 
for all bases.

Best,
J.

On Mar 16, 2011, at 7:59 PM, Austin Paul wrote:

> Hi,
> 
> I would like to extract raw counts from tophat output.  Does anyone know a 
> way to do this in Galaxy?
> 
> Thanks!
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