Hi Vasu, Thanks for your response. I realize tophat and bowtie are different. But my question was concerning what seemed to me to be divergent results from mapping with tophat and bwa (which I also realize are different). bwa seemed to map around 4x the reads that tophat mapped using the same reference. Should this not come as a surprise? Austin On Wed, Apr 27, 2011 at 2:30 PM, vasu punj <punjv@yahoo.com> wrote:
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 <austinpa@usc.edu>* wrote:
From: Austin Paul <austinpa@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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