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14 Sep 2015 2 Jan 2012 Please Note If you have questions about how to use Cufflinks or software, please email tophat.cufflinks@gmail.com, though we ask you to Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned The Cufflinks suite of tools can be used to perform a number of different types of analyses for RNA-Seq experiments. The Cufflinks suite includes a number of 28 Oct 2009 FASTqc > Tophat > Cufflinks > Cuffdiff. Creating an SGE script for your workflow. RNA-seq. Gene expression can be estimated by measuring RNA in the cell Jason has worked out a great tutorial for RNA-seq analysis with tophat/cufflinks and willing to share with all of us. We appreciate his contribution on behalf of 8 Mar 2013 17 Jan 2017 The main aim of this tutorial is to illustrate how to use Cufflinks tools for differential expression analysis. Firstly, let's move to the command line Contribute to cole-trapnell-lab/cufflinks development by creating an account on GitHub.