Bioinformatics Data Analysis
All Projects
Run Parameters
Parameters used during the run:

Result description.

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/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

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