Differentially expressed gene analysis of RNA-seq data using R

Chapter 1 NGS data exploration

When working on RNA-Seq data using R the short reads are usually mapped to the reference genome using a genome mapper and the DNA sequences themselves are handled by the mapping software. However, it is useful to know that we can perform a number of analyses on the DNA sequences themselves in R. The QC analysis and evaluation of the sequence collection content can be managed as well.

There are a number of different DNA sequencing platforms in use that have their own characteristics and challenges.