Hello Bin, If your data is RNA-seq, then this tutorial can get you started with the basics: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq Hopefully this helps, Best, Jen Galaxy team On 9/26/11 8:46 AM, Binbin You wrote:

Hi All,

Now I have two Paired-End samples data ( they are Next Generation Sequence Data and fastq format) generated from Illumina GA II. Let's say Data Lane1 and Data Lane2. After Quality trimming and Adapter trimming, I want to check the Genes Differential Expression between these two samples. How could I do that in Penn State version Galaxy or other versions with only having Reference File? Thanks a lot in advance!

Best wishes, Bin

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