nicolasDelhomme

Reproducible research

The goal of this git crash course intro is to introduce you to tools for reproducible research (RR). To ensure RR, we need at least two components:

1. the data (that has to be published upon manuscript acceptance by most journal standards)
2. the code (yes how you ran your analysis!)

There are extra components (tools, version, providing these in containers), but let's focus on 2.

Git

Intro

That book is a great resource. We only need to know a little to get started. In your own time, look at Chapter 1, section 1. to 4 and once you start using it Chapter 2 is all you need (99% of the time).

nicolasDelhomme

Expression Quantification

Intro

We have now generated, assessed and annotated our de-novo transcriptome assembly. Yay! So let's start using it.

The trinity wiki describes many of the downstream analyses that can be conducted and provides tools for doing so.

But, presumably, one of the first steps will be to use it to quantify the expression of the different samples we used to build our assembly.

For that we will use a pseuso-aligner, namely salmon.