I have Cufflink generated .gtf files on 2 different Rna-seq datasets , each belonging to a different tissue.
ex: adrenal1 and adrenal2 datasets ex: brain 1 and brain 2 datasets.
i need to analyse DGE : differential gene expression between the 2 samples that is between adrenal and brain tissue.
Am i supposed to add the .gtf files of both tissues together for cuffmerge??
pls see the snapshot : http://s31.postimg.org/bfwh37ofv/biostar_cuffmerge.jpg