Figure 2.

An overview of the Tuxedo protocol. In an experiment involving two conditions, reads are first mapped to the genome with TopHat. The reads for each biological replicate are mapped independently. These mapped reads are provided as input to Cufflinks, which produces one file of assembled transfrags for each replicate. The assembly files are merged with the reference transcriptome annotation into a unified annotation for further analysis. This merged annotation is quantified in each condition by Cuffdiff, which produces expression data in a set of tabular files. These files are indexed and visualized with CummeRbund to facilitate exploration of genes identified by Cuffdiff as differentially expressed, spliced, or transcriptionally regulated genes. FPKM, fragments per kilobase of transcript per million fragments mapped.