How Did We Do?

Now, the moment we've all been waiting for. How do our outputs, albeit with slightly different software versions and other adjustments to just make things work compare to the conclusions drawn by the authors. Are the numbers just somewhat off, or do we have bigger fish to fry? ...or bigger larvae to freeze?

First, we'll talk about how well we were able to recapitulate the numbers for differential expression using the bash pipeline. This is the first set of steps using Cufflinks, Bowtie, Cuffmerge, etc.

Next, we'll dive into some data analysis with Jupyter notebooks, using our data as well as the converted .xlsx data provided by the authors from their analysis. We'll do most of this in Python, but also show some in R, if that's your language of choice.