Bioinformatics Data Analysis

Results generated by running the recipe.

Parameters used during the run:

File List
Files created by the recipe run:
counts.txt 2.6 KB
deseq1.r 2.4 KB
log.txt 5.5 KB
names.txt 36 bytes
recipe.sh 1.5 KB
refs/22.fa 49.3 MB
refs/22.gtf 26.0 MB
Output Messages
Messages printed to the standard output stream:
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
Other Messages
Messages printed to the standard error stream:
+ 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

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