[galaxy-user] cuffdiff

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