Use the replicates option (yes, a bit of a misnomer) and put each Tophat run in its own group. This will produce a tabular file with FPKM for each group/run. Best, J. On Nov 12, 2012, at 10:05 AM, Vevis, Christis wrote:

Hi,

I got confused while trying to perform Cuffdiff for my RNA sequencing analysis. So I have five different samples which were sequenced. I used tophat to create the bam files and cufflink to create the assembled trancripts. Then I uded Cuffmerge to merge them in one file and then I wanted to do Cuffdiff with that merged file. What shall I choose for the ‘’SAM or BAM file of aligned RNA-Seq’’ option? I have the 5 options from the 5 tophat actions on my 5 samples. All I want in the end is an excel table showing the number of hits from each sample (and not necessary a comparison of them).

Regards

Kristis Vevis, PhD Student Cell Biology UCL Institute of Ophthalmology 11-43 Bath Street London EC1V 9EL, UK 020 7608 4067

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