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I believe (but might be wrong) that you have been told before that the pipeline tophat-cufflinks-cuffmerge is no longer the accepted best pipeline for RNA-seq analysis and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.)