#!/usr/bin/env bash

FILES=$(cat ./data/SampleInputFileLinks.txt)
for file in $FILES; do
    # --no-clobber, do not download if file already exists.
    wget -nc $file
done

hisat2-build -p 8 genome.fa hg38_hisat
hisat2 –x index -1 sample1_trim_R1.fq -2 sample1_trim_R2.fq –U unpair.fq –S sample1.sam
htseq-count –r sample1.sam sample2.sam samplen.sam hs.gff > count_matrix.txt

Rscript dge_analysis.r