Analysis

Bioinformatics

FastQC  v0.11.5  \cite{data} was used for quality control of reads. 
Trim galore 
HISAT2 v 2.1.0 \cite{Kim2015} for alignment
RSeQC \cite{Wang2012}
Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67 \cite{McKenna_2010}