Here’s what I do, in order, to set my computer up to be able to install software that we use in the class. Disclaimer: I just got a new work laptop, so it doesn’t have much of an environment on it yet. I can’t know what you’ve done to your computer in the past, and so some of these things may not work for you if your environment’s already like this: Administrator privileges 2. xcode Install the xcode libraries that…
This tutorial is my version of the workflow for analysis of the Synechocystis PCC6803 gene expression data using Trinity and Corset. Disclaimer: walking through the workflow shows that there is plenty to be skeptical about in this dataset or at least in the stat and exp samples. So we should definitely talk about what to look for. Define the problem To start off with, let’s just pretend that this Synechocystis data set has no reference genome. How will we determine where the reads belong…
Remember the chloroplast variant calling tutorial? Turns out, you can implement the same thing in Galaxy. (Sort of). Since the chloroplast files are very small, I’m recommending you do this on Galaxy Main, because some of the tools in this sequence mysteriously did not work in my own Galaxy, and those are not always issues that can be fixed in real time. Identify the tools If you think back to the tools involved in our simple variant calling pipeline, the major steps…