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,
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:
Thank you very much. I already used Galaxy to prepare the mapping by
bowtie for solid. I saw the tophat for solid on the test server and will
try it. Do I need to run cufflink after that?
Please accept my utmost appreciation!