Results generated by running the recipe.
Parameters used during the run:
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 refs/22.fa refs/22.gtf refs/ERCC92.fa refs/ERCC92.gtf
+ 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/22.fa + GTF=refs/22.gtf + hisat2-build refs/22.fa refs/22.fa + parallel -j 1 echo '{1}_{2}' ::: UHR HBR ::: 1 2 3 + mkdir -p bam + cat names.txt + parallel 'hisat2 refs/22.fa -1 reads/{}_R1.fq -2 reads/{}_R2.fq | samtools sort > bam/{}.bam' + featureCounts -p -a refs/22.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 + Rscript draw-heatmap.r + cat norm-matrix-deseq1.txt