Hello Di, Both Bowtie and Tophat will map sequences, with Tophat being preferred for RNA-seq data. If you wish to do downstream analysis, then using the Cuff* tools would be the next steps. Each of these tools has an associated help description that explains the inputs/outputs. Thanks for using Galaxy, Jen Galaxy team ps. Please send all questions directly to the mailing lists unless they contain private data/links. On 9/1/11 10:45 AM, Di Nguyen wrote: -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support