Re: [Gmod-ajax] next generation sequencing visualization

[Mitch S. <mit...@be...>]

Ann Loraine wrote:
> http://bowtie-bio.sourceforge.net/index.shtml
>
> My lab is using it in combination with another program from the
> Salzberg lab titled Top Hat, which aims to solve the "how do we map
> short reads across introns" problem.
>   

I skimmed the web pages for bowtie (Burrows-Wheeler!  very cool) and top 
hat.  Does top hat generate its bed and wig output in alignment coords 
or refseq coords?  What do you currently do with the top hat output?

Mitch