Bioinformatics Data Analysis

Results generated by running the recipe.

Parameters used during the run:

File List
Files created by the recipe run:
counts.txt 8.3 MB
deseq1.r 2.4 KB
log.txt 7.1 KB
mock.txt 5.8 MB
over25.txt 1.9 MB
recipe.sh 3.3 KB
valid.txt 1.5 MB
zikv.txt 5.8 MB
Output Messages
Messages printed to the standard output stream:


        
Other Messages
Messages printed to the standard error stream:
+ PROJECT=PRJNA313294
+ GTF=/home/www/refs/Homo_sapiens.GRCh38.96.chr.gtf
+ RUNINFO=runinfo.all.csv
+ SINGLE=runinfo.single.csv
+ PAIRED=runinfo.paired.csv
+ READNUM=1000000
+ REF=/home/www/refs/Homo_sapiens.GRCh38.cdna.all.fa
+ IDX=/home/www/refs/Homo_sapiens.GRCh38.cdna.all.idx
+ esearch -db sra -query PRJNA313294
+ efetch -format runinfo
+ cat runinfo.all.csv
+ cut -f 1 -d ,
+ grep 'SRR.*SINGLE'
+ cat runinfo.all.csv
+ cut -f 1 -d ,
+ grep 'SRR.*PAIRED'
+ cat runinfo.single.csv
+ parallel fastq-dump -X 1000000 -O reads
+ cat runinfo.paired.csv
+ parallel fastq-dump -X 1000000 --split-files -O reads
+ kallisto index -i /home/www/refs/Homo_sapiens.GRCh38.cdna.all.idx /home/www/refs/Homo_sapiens.GRCh38.cdna.all.fa

[build] loading fasta file /home/www/refs/Homo_sapiens.GRCh38.cdna.all.fa
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
        from 1431 target sequences
[build] warning: replaced 5 non-ACGUT characters in the input sequence
        with pseudorandom nucleotides
[build] counting k-mers ... done.
[build] building target de Bruijn graph ...  done 
[build] creating equivalence classes ...  done
[build] target de Bruijn graph has 1131887 contigs and contains 109544288 k-mers 

+ mkdir -p results
+ cat runinfo.single.csv
+ parallel kallisto quant -i /home/www/refs/Homo_sapiens.GRCh38.cdna.all.idx -o 'results/{}' --single -l 187 -s 70 'reads/{}.fastq'
+ cat runinfo.paired.csv
+ parallel kallisto quant -i /home/www/refs/Homo_sapiens.GRCh38.cdna.all.idx -o 'results/{}' -l 187 -s 70 'reads/{}_1.fastq' 'reads/{}_2.fastq'
+ cat runinfo.single.csv runinfo.paired.csv
+ parallel 'cut -f 1,4 results/{}/abundance.tsv > results/{}.txt'
+ paste results/SRR3191542.txt results/SRR3191543.txt results/SRR3194428.txt results/SRR3194429.txt
+ cut -f 1,2,4,6,8
+ paste results/SRR3191544.txt results/SRR3191545.txt results/SRR3194430.txt results/SRR3194431.txt
+ cut -f 1,2,4,6,8
+ paste mock.txt zikv.txt
+ cut -f 1-5,7-11
+ cat counts.txt
+ awk ' ($2+$3+$4+$5+$6+$7+$8+$9) > 25 { print $0 } '
+ cat over25.txt
+ awk ' { printf("%s\t%4.0f\t%4.0f\t%4.0f\t%4.0f\t%4.0f\t%4.0f\t%4.0f\t%4.0f\n", $1, $2, $3, $4, $5, $6, $7, $8, $9) } '
+ wget -q -nc http://data.biostarhandbook.com/rnaseq/code/deseq1.r
+ cat valid.txt
+ Rscript deseq1.r 4x4
+ 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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