Why are we interested in reproducibility?

Reproducibility is one of the basic tenets of science. There's a reason why that was part of your grand introduction to science and the scientific method, perhaps in middle school. It's through peer review and the scientific process that we really keep ourselves accountable in science, and it is this collaborative process that drives science forward (Yaffe, 2015).

What's more, reproducibility in science, especially in software and bioinformatics, as you'll see, can be hard. And the things most worth doing in science are the difficult things. By attempting reproduce a paper (or even just checking the data availability for a new paper), we can make science more efficient and more accessible for everyone. It also teaches us new scientific tools.

It is truly a skill to be able to read a bioinformatics paper, especially one about software development, and be able to understand what the authors are talking about when they attempt trace their steps in words and/or diagrams. Plus, if you do anything related to transcriptomics, there's an extremely high probability you have and/or will use a lot of the tools described in this tutorial. While a lot of bioinformatics software is out there, there are also many tried and true favorites, and Cufflinks, Bowtie and TopHat are certainly among them.

1. Yaffe, M. B. (2015). Reproducibility in science. American Association for the Advancement of Science.