Introduction to tophat cufflinks workflow
The tophat-cufflinks-cuffdiff analysis pipeline
From: http://dx.doi.org/10.1038/nprot.2012.016, Modified by NA
Alternate tools and pipelines
From: http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html
A comparison of different rna-seq analysis tools
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