Hello Irene, Both can be used with a custom reference genome - there is no difference between the tools in that regard. However, Bowtie is for mapping DNA and Tophat is for mapping RNA. More details are on the tool forms, including links to the primary tool home pages. Hopefully this helps, Jen Galaxy team On 8/11/12 10:09 AM, i b wrote:

Hi all, what is the difference between using "NGS:mapping-------Map with Bowtie for Illumina" and "NGS: RNA analysis---------Tophat for Illumina" when mapping reads against a reference/custom genome?

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