Hello Candace, For RNA-seq data, a better choice would be "NGS: RNA Analysis -> Tophat for SOLiD" then the downstream Cuff* tools. This is also only on test (http://test.g2.bx.psu.edu) for now, which has usage limits (10G max), but you could certainly try the tools out and see they work for you. If they do, then you could consider setting up your own instance: http://galaxyproject.org/wiki/Test http://galaxyproject.org/wiki/Big%20Picture/Choices Help with RNA-seq analysis can be found at: http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq Hopefully this helps to get you started, Jen Galaxy team On 9/13/11 12:59 PM, Candace Seeve wrote:

I am new to RNA-Seq and trying to map ABI SOLID paired-end reads. I've read that BFAST + BWA is a good program for this. I have found BFAST on the galaxy test site. Is it possible to map paired end reads using the BFAST version there? Could someone help me with this workflow?

Thanks very much in advance.

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