Though Tophat calls in Bowtie but they are different mapping tools. Details can 
be found in mannual of Tophat. For RNA-seq one may be stick with Tophat.
 
Vasu

--- On Wed, 4/27/11, Austin Paul <austi...@usc.edu> wrote:


From: Austin Paul <austi...@usc.edu>
Subject: [galaxy-user] mapping with tophat vs. bwa
To: galaxy-user@lists.bx.psu.edu
Date: Wednesday, April 27, 2011, 4:20 PM


Hello,

I am getting what seems to me to be strange results using two different mapping 
tools in Galaxy.  I am mapping illumina RNA-seq data and with tophat, while 
setting # alignments to 1, I get around 15-20% reads mapping.  And when I use 
bwa, I am getting around 75% reads mapping.  My reference is a collection of 
ESTs so the strength of tophat being a spliced read mapper is probably not 
being utilized, but I am surprised by the difference in the number of reads 
mapping between the two.  Any thoughts?

Austin

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