Description

A tutorial R package that describes the pre-processing of RNA-Seq data - from the raw (FASTQ) data to the alignment (mapping) to a reference genome - and its subsequent differential expression analysis at the gene and transcript level.

Installation

First installed the dependencies. Then check that the package can "Build and Reload"

Preparation

Go to the vignettes folder

1. In the Templates folder:
   1. In Tutorial.Rmd: modify the title and decide which chapters should be included
   2. In ChapterTemplate.Rmd: modify the title
2. In the Chapters foolder:
   1. Modify/Add Rmd files
   2. Modify the path of the data (e.g. DayXX to match the course schedule)
3. In the vignettes folder, run

       R CMD make
   

If it works, save the html page you need, as well as the Rscript from the RnaSeqTutorial/inst/doc directory.

Caveats

inv block only numbers inv-XXXX

When building if it fails at the stage at which it creates the RnaSeqTutorial.html page, be careful to restore the original structure of the vignette folder (i.e. copy Chapters.orig back to Chapters)

Also the package need to be preinstalled so that the data, etc. is available.