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Old 11-07-2013, 11:40 AM   #4
feralBiologist
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Location: UK

Join Date: Jun 2011
Posts: 61
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I stopped using cufflinks/cuffdiff 3 months ago as the latest version was producing implausible results. I would recommend using tophat2 + htseq-count + edgeR (or DESeq). I based my workflow on this nice tutorial: http://www-huber.embl.de/pub/pdf/nprot.2013.099.pdf
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