Using Sleuth R package for differential expression analysis in Atmosphere, walkthrough example

Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly. We will use the output from the StringTie step that created the ballgown input files.Here we are doing a pairwise comparison for differential expression in sensitive genotype(IS20351) under Drought Stress(DS) and Well Watered(WW) condition. We have 3 replicates under each condition