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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