Hi,
  Thanks very much.  I've tried this, but one thing I have noticed is that if I 
do the initial mapping with BWA vs. Bowtie the # of variants I get is much 
larger with BWA.  I have seen mention on the web that you need to change the 
quality score annotation for BWA before running SAMtools, but not sure 
precisely how to do this.  any thoughts?

Rich



________________________________
From: Jeremy Goecks <jeremy.goe...@emory.edu>
To: Richard Mark White <whit...@yahoo.com>
Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
Sent: Sunday, August 28, 2011 2:18 PM
Subject: Re: [galaxy-user] rna-seq mutation detection


Rich,

Given that you're analyzing your RNA-seq data using Galaxy, I'd guess that 
you're using Tophat to map your reads onto on reference genome. If this is the 
case, then you can use the BAM files produced by Tophat to generate variation 
data for each sample. The variation tools that you'll want to look at are 

[NGS: SAM Tools-->]Generate Pileup
[NGS: GATK Tools-->]Unified Genotyper (only avaiable on our test server and 
still in beta)

The outputs for each tool produce a consensus base for each potential variation 
site, and you can compare the consensus base for each sample to look for 
differences.

If you're doing de novo assembly of your RNA-seq data to look for variation, 
you'll need to use tools that are not currently available in Galaxy.

Good luck,
J.




On Aug 18, 2011, at 12:22 PM, Richard Mark White wrote:

Hi,
>  I am trying to look at differences between two RNA-seq samples to see if 
>there are mutations in one of them relative to the other (i.e. not in 
>comparison to a reference genome).  Does anyone know of a way to do this 
>within galaxy?  Any help is appreciated!
>
>
>rich
>
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