There are two things: first, the Bowtie for Illumina and Bowtie for SOLiD wrappers use different data tables (bowtie_indexes as opposed to bowtie_indexes_color), which refer to different loc files (bowtie_indexes.loc and bowtie_indexes_color.loc, respectively). Secondly, although this won't

Ahh right.  I totally missed that.  It's working now, thanks.
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