# Introduction

This vignette provides the implementation of the procedure described in point 
7 of our __Guidelines for RNA-Seq data analysis__[^1] protocol available from
the __Epigenesys__ [website](http://www.epigenesys.eu).

Briefly, it details the step necessary to:
1. create a non-redundant annotation

2. count reads per feature

3. pre-analyse the data, i.e. assess the pertinence of the samples' 
charateristics in the light of their biological provenance; _i.e._ in other words
perform a so called _"biological QA"_ using assessment methods such as _Principal
Component Analysis_, _Multi-dimensional Scaling_, _Hierarcical Clustering_, _etc._

The aim of this vignette is to go through these steps using the __easyRNASeq__
package, hence the rationale of the implementation will not be discussed, albeit
relevant litterature will be pointed at when necessarry.

Throughout this vignette we are going to replicate the analysis conducted in
Robinson, Delhomme et al.[@Robinson:2014p6362], a study looking at _sexual
dimorphism_ in _Eurasian aspen_.

To perform the listed steps, we need to instantiate a number 
of objects to store the minimal set of parameters describing the conducted 
__RNA-Seq__ experiment, _e.g._ the BAM files location, the annotation location 
and type, the sequencing parameters, _etc._

To get started with this process, we load the package into our R session:

```{r library}
library(easyRNASeq)
```

before instantiating an __AnnotParam__ object informing on the location and type
of the annotation to be used.

```{r vignetteData, echo=FALSE}
vDir <- vignetteData()
```
----