this github has my annotated markdown with all of the scripts that were run to generate the data and images in the paper. This is a git hub of the RNA alaysis performed to obtain Differentiatlly expressed genes. The upstream sequencing cleaning an dalignment were provided by New York Genome center. The feature Counts data from ther analysis was used for the analysis. RNA abundance was measured by mapping with Bowtie2.
Quality control was performed using Picard and RSeQC.
The reads were aligned with STAR (version 2.5.2a), and annotated genes were quantified with featureCounts (v1.4.3-p1).