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