Introducing Blacktie: a simpler way to do RNA-seq using Tophat/Cufflinks/CummeRbund

The Tophat/Cufflinks/CummeRbund group of programs (termed the "Tuxedo Protocol") makes quality RNA-seq analysis doable once you understand the process. But what about when it's time for you to leave the lab and you need to "train" someone else to repeat your process? It can be a nightmare.

Especially if the trainee is not yet comfortable with the command line. This is why I wrote the Blacktie pipeline software. Its goals are to streamline and simplify the complex task of analyzing full RNA-seq experiments using these programs; to automatically record settings used and program output messages in a way that users can track them to data later; provide a base set of functions and classes that will allow users to create custom pipelines easily by editing a single file (or if they want: writing their own custom scripts).