Re: [galaxy-user] mapping with tophat vs. bwa

2011-04-28 Thread Kevin Lam
, 2011 at 2:30 PM, vasu punj 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 * wrote:

Re: [galaxy-user] mapping with tophat vs. bwa

2011-04-27 Thread Austin Paul
- On *Wed, 4/27/11, Austin Paul * wrote: > > > From: Austin Paul > 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 u

Re: [galaxy-user] mapping with tophat vs. bwa

2011-04-27 Thread vasu punj
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 wrote: From: Austin Paul Subject: [galaxy-user] mapping with tophat vs. bwa To: galaxy-user

[galaxy-user] mapping with tophat vs. bwa

2011-04-27 Thread Austin Paul
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