This protocol describes in detail how to use TopHat and Cufflinks to perform RNA-seq analyses. It also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-seq analysis results.

Nature Protocols 2012: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ~1 h of hands-on time.