Hello, On 4/28/11 9:21 PM, puvan001@umn.edu wrote:

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

Please try: "NGS: SAM Tools -> flagstat provides simple stats on BAM files"

2. I am aware that Cuffdiff is used to find the differences in expression. How do I combine replicates (3) of different treatments ?

Set the "NGS: RNA Analysis -> Cuffdiff" form so that the second choice, "Perform replicate analysis:" is "Yes". The ability to add/define groups from your history will pop up when the form modifies in response to this selection. Best wishes for your research, Jen Galaxy team

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