Re: [galaxy-dev] Installing Prebuilt Indexes for "Tophat for Illumina" - What to do for color space files?

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.