Job View: Results for How to analyze RNA-Seq spiked control samples with kallisto

Results for How to analyze RNA-Seq spiked control samples with kallisto

Results generated by running the recipe.

Completed

• Runtime 17 seconds • updated 5.0 years ago by Istvan Albert

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/ERCC92.fa + IDX=refs/ERCC92.idx + kallisto index -i refs/ERCC92.idx refs/ERCC92.fa + parallel -j 1 echo '{1}_{2}' ::: UHR HBR ::: 1 2 3 + mkdir -p results + cat names.txt + parallel 'kallisto quant -i refs/ERCC92.idx -o results/{} reads/{}_R1.fq reads/{}_R2.fq' + cat names.txt + parallel cp 'results/{}/abundance.tsv' 'results/{}.abundance.tsv' + cut -f 1,4,9,14,19,24,29 + paste results/HBR_1.abundance.tsv results/HBR_2.abundance.tsv results/HBR_3.abundance.tsv results/UHR_1.abundance.tsv results/UHR_2.abundance.tsv results/UHR_3.abundance.tsv + wget -q -nc http://data.biostarhandbook.com/rnaseq/code/deseq1.r + cat 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

Bioinformatics Data Analysis