Hello Bao, For RNA-seq analysis, removing any reads would be problematic since this would interfere with expression/abundance calculations. For mapping, TopHat is the preferred alignment tool for spliced RNA data. BWA and Bowtie are tools better suited for DNA mapping. For Prokaryote genomes, the choice of which alignment tool to use may be more flexible (splicing would not be an issue), but understanding the parameters for the tool options and how to tune appropriately (e.g. for a circular genome) would be important to research and test out. For more details about TopHat, please see the author's web site (including an FAQ) at: http://tophat.cbcb.umd.edu/. A help email is also available: tophat.cufflinks@gmail.com. Best, Jen Galaxy team On 2/15/12 9:39 AM, vang0280@umn.edu wrote:

Dear all,

When is it necessary to remove duplicate reads from your RNA Seq analysis? Is it required for Tophat versus BWA versus Bowtie?

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