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

2013-06-08T00:03:39Z (GMT) by Augustine Dunn
<p>Leveraging multiple fastQ files full of RNA-seq reads into a coherent picture of gene expression and transcript models is a multi-step process. It requires the organization and coordination of many files of different types through many different program calls and output steps. Each step might take hours or days depending on your input data. Then, as you are writing up your work, sometimes weeks/months later, you see that a new version of the programs you use has come out. Do you need to re-run your analysis? What settings DID you use back then?</p> <p> </p> <p>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.</p> <p> </p> <p>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).</p>