What does Cufflinks do?

This tool takes TopHat-processed short reads and assembles them into as many mRNA transcripts as it can, and as complete as possible; then Cufflinks measures the abundance of each transcript (Source: MiniMouse tutorial)

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols (Source https://ngs.csr.uky.edu/Cufflinks)

• note to self: TopHat takes RNA-seq data and compares to known genome, Cufflink assembles the data and tells us how much of it there is --> greater abundance = greater expression