Diagram of Abbreviated Tophat/Cufflinks Inputs and Outputs

This figure demonstrates the complexities of a typical RNA-seq experiment as analyzed with the "Tuxedo Protocol". It models a fairly simple two condition experiment with each condition having three replications. It is "abbreviated" in that it only displays the output files that will be used in the next step for all steps except the 'cuffdiff' step. The complete output of 'cuffdiff' is included to demonstrate the final challenge of integrating the data which exists in multiple cross-referenced files.