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 > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
