I am new to Galaxy and I am not sure whether these topics were discussed earlier. I followed the steps up to cufflinks and I did not have any problems. Thanks for the RNA seq tutorial. My questions are 1. How do I know the number of reads mapped against the reference genome used after Top Hat mapping 2. I am aware that Cuffdiff is used to find the differences in expression. How do I combine replicates (3) of different treatments ?

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