>
> I see where I would use the *.ebwt files in the bowtie_index.loc file.
> But I'm not sure what to reference in the bowtie_index_color.loc
> file? (The same *.ebwt files??)
You need to download the colorspace indices separately:
http://bowtie-bio.sourceforge.net/index.shtml
Good luck,
J.
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