Hi guys, a bit of confusion about how to give cuffdiff certain outputs: having 1 control and 8 tumour samples which I consider biological replicates (not technical replicates), how shall give the input to cuffdiff?
If I want to use cuffcompare as gtf: shall I cuffcompare all 8samples plus the control and then run cuffdiff using this gtf? When adding the bam files, shall I have to make 8 groups plus control groups? or one groups with 8 bams and second group with the control bam? Much appreciated an answer!! Thanks ib ___________________________________________________________ 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/
