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,
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