Can it be integrated into galaxy ? I found another tool that does this at http://galaxy.fml.mpg.de/

Under their SAM tools they have a pileup to wiggle conversion tool 

On Wed, Jan 12, 2011 11:01 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:

 I can't find any mention of a program called 'wiggles' in the source
> code distribution of bowtie 0.12.7, or out install of 0.12.3. Could
> someone point me to the location of the program in the bowtie file
> structure, or failing that a website for it?

wiggles is in the Tophat distribution, not the Bowtie distribution.

Thanks,
J.
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