+ URL=http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz
+ LOG=runlog.txt
+ tar xz
+ curl -s http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz
+ REF=refs/22.fa
+ IDX=refs/22.fa
+ GTF=refs/22.gtf
+ hisat2-build refs/22.fa refs/22.fa
+ samtools faidx refs/22.fa
+ BAMDIR=xbam
+ mkdir -p xbam
+ parallel -N 2 'hisat2 refs/22.fa -1 {1} -2 {2} 2>> runlog.txt' '|' 'samtools sort 2>>runlog.txt' '>' 'xbam/{1/.}.bam 2>> runlog.txt'
+ ls -1 reads/HBR_1_R1.fq reads/HBR_1_R2.fq reads/HBR_2_R1.fq reads/HBR_2_R2.fq reads/HBR_3_R1.fq reads/HBR_3_R2.fq reads/UHR_1_R1.fq reads/UHR_1_R2.fq reads/UHR_2_R1.fq reads/UHR_2_R2.fq reads/UHR_3_R1.fq reads/UHR_3_R2.fq
+ ls -1 xbam/HBR_1_R1.bam xbam/HBR_2_R1.bam xbam/HBR_3_R1.bam xbam/UHR_1_R1.bam xbam/UHR_2_R1.bam xbam/UHR_3_R1.bam
+ parallel 'samtools index {} 2>> runlog.txt'
+ featureCounts -a refs/22.gtf -g gene_name -o counts_full.txt xbam/UHR_1_R1.bam xbam/UHR_2_R1.bam xbam/UHR_3_R1.bam xbam/HBR_1_R1.bam xbam/HBR_2_R1.bam xbam/HBR_3_R1.bam
+ mkdir -p code
+ cd code
+ curl -sO http://data.biostarhandbook.com/rnaseq/code/deseq1.r
+ cd code
+ curl -sO http://data.biostarhandbook.com/rnaseq/code/deseq2.r
+ cd code
+ curl -sO http://data.biostarhandbook.com/rnaseq/code/edger.r
+ cd code
+ curl -sO http://data.biostarhandbook.com/rnaseq/code/draw-heatmap.r
+ cat counts_full.txt
+ cut -f 1,7-12
+ cat counts_simplified.txt
+ Rscript code/deseq1.r 3x3
+ cat norm-matrix-deseq1.txt
+ Rscript code/draw-heatmap.r
+ cat counts_simplified.txt
+ Rscript code/deseq2.r 3x3
+ cat norm-matrix-deseq2.txt
+ Rscript code/draw-heatmap.r
+ cat counts_simplified.txt
+ Rscript code/edger.r 3x3
+ cat norm-matrix-edgeR.txt
+ Rscript code/draw-heatmap.r