+ 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
+ IDX=/home/www/refs/grch38/genome
+ efetch -format runinfo
+ esearch -db sra -query PRJNA313294
+ cat runinfo.all.csv
+ cut -f 1 -d ,
+ grep 'SRR.*SINGLE'
+ cut -f 1 -d ,
+ cat runinfo.all.csv
+ 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
+ mkdir -p bam
+ CPUS=4
+ cat runinfo.paired.csv
+ parallel 'hisat2 -p 4 -x /home/www/refs/grch38/genome -1 reads/{}_1.fastq -2 reads/{}_2.fastq 2>> log.txt | samtools sort > bam/{}.bam'
+ cat runinfo.single.csv
+ parallel 'hisat2 -p 4 -x /home/www/refs/grch38/genome -U reads/{}.fastq 2>> log.txt | samtools sort > bam/{}.bam'
+ parallel samtools index '{}'
+ ls -1 bam/SRR3191542.bam bam/SRR3191543.bam bam/SRR3191544.bam bam/SRR3191545.bam bam/SRR3194428.bam bam/SRR3194429.bam bam/SRR3194430.bam bam/SRR3194431.bam
+ MOCK=(SRR3191542 SRR3191543 SRR3194428 SRR3194429)
+ ZIKV=(SRR3191544 SRR3191545 SRR3194430 SRR3194431)
+ for SRR in '${MOCK[@]}'
+ MOCK_BAMS+='bam/SRR3191542.bam '
+ for SRR in '${MOCK[@]}'
+ MOCK_BAMS+='bam/SRR3191543.bam '
+ for SRR in '${MOCK[@]}'
+ MOCK_BAMS+='bam/SRR3194428.bam '
+ for SRR in '${MOCK[@]}'
+ MOCK_BAMS+='bam/SRR3194429.bam '
+ for SRR in '${ZIKV[@]}'
+ ZIKV_BAMS+='bam/SRR3191544.bam '
+ for SRR in '${ZIKV[@]}'
+ ZIKV_BAMS+='bam/SRR3191545.bam '
+ for SRR in '${ZIKV[@]}'
+ ZIKV_BAMS+='bam/SRR3194430.bam '
+ for SRR in '${ZIKV[@]}'
+ ZIKV_BAMS+='bam/SRR3194431.bam '
+ featureCounts -g gene_name -a /home/www/refs/Homo_sapiens.GRCh38.96.chr.gtf -o counts.txt bam/SRR3191542.bam bam/SRR3191543.bam bam/SRR3194428.bam bam/SRR3194429.bam bam/SRR3191544.bam bam/SRR3191545.bam bam/SRR3194430.bam bam/SRR3194431.bam
+ cat counts.txt
+ cut -f 1,7-14
+ wget -q -nc http://data.biostarhandbook.com/rnaseq/code/deseq1.r
+ cat simple_counts.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