+ URL=http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz + wget -q -nc http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz + tar zxvf griffith-data.tar.gz + REF=refs/ERCC92.fa + GTF=refs/ERCC92.gtf + hisat2-build refs/ERCC92.fa refs/ERCC92.fa + parallel echo '{1}_{2}' ::: UHR HBR ::: 1 2 3 + mkdir -p bam + cat names.txt + parallel 'hisat2 refs/ERCC92.fa -1 reads/{}_R1.fq -2 reads/{}_R2.fq | samtools sort > bam/{}.bam' + featureCounts -a refs/ERCC92.gtf -g gene_name -o counts.txt bam/HBR_1.bam bam/HBR_2.bam bam/HBR_3.bam bam/UHR_1.bam bam/UHR_2.bam bam/UHR_3.bam + wget -q -nc http://data.biostarhandbook.com/rnaseq/code/deseq1.r + cat counts.txt + cut -f 1,7-12 + cat simple_counts.txt + Rscript deseq1.r 3x3 + wget -q -nc http://data.biostarhandbook.com/rnaseq/code/draw-heatmap.r + cat norm-matrix-deseq1.txt + Rscript draw-heatmap.r