Bioinformatics Recipe Cookbook

Run Parameters
Parameters used during the run:
  • Bioproject number: PRJNA257197
Output Messages
Messages printed to the standard output stream:
Read 1000 spots for SRR1972921
Written 1000 spots for SRR1972921
Read 1000 spots for SRR1972917
Written 1000 spots for SRR1972917
Read 1000 spots for SRR1972918
Written 1000 spots for SRR1972918
Read 1000 spots for SRR1972919
Written 1000 spots for SRR1972919
Read 1000 spots for SRR1972920
Written 1000 spots for SRR1972920

SAM file header:
@HD	VN:1.5	SO:queryname
@RG	ID:GROUP-SRR1972917	SM:SAMPLE_SRR1972917	LB:LIB-SRR1972917
@RG	ID:GROUP-SRR1972918	SM:SAMPLE_SRR1972918	LB:LIB-SRR1972918
@RG	ID:GROUP-SRR1972919	SM:SAMPLE_SRR1972919	LB:LIB-SRR1972919
@RG	ID:GROUP-SRR1972920	SM:SAMPLE_SRR1972920	LB:LIB-SRR1972920
@RG	ID:GROUP-SRR1972921	SM:SAMPLE_SRR1972921	LB:LIB-SRR1972921

Number of alignments with read group: GROUP-SRR1972919
2000
Other Messages
Messages printed to the standard error stream:
+ PROJECT=PRJNA257197
+ N=5
+ esearch -db sra -query PRJNA257197
+ efetch -format runinfo
+ cat runinfo.txt
+ cut -f 1 -d ,
+ grep SRR
+ head -5
+ mkdir -p reads
+ cat selected.txt
+ parallel fastq-dump -O reads -X 1000 --split-files '{}'
+ mkdir -p bam
+ cat selected.txt
+ parallel 'picard FastqToSam F1=reads/{}_1.fastq F2=reads/{}_1.fastq O=bam/{}.bam  RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} QUIET=true 2>> log.txt'
+ samtools merge -f all.bam bam/SRR1972917.bam bam/SRR1972918.bam bam/SRR1972919.bam bam/SRR1972920.bam bam/SRR1972921.bam
+ echo ''
+ echo 'SAM file header:'
+ samtools view -H all.bam
+ echo ''
+ echo 'Number of alignments with read group: GROUP-SRR1972919'
+ samtools view -c -r GROUP-SRR1972919 all.bam
+ samtools fastq -t -1 all1.fq -2 all2.fq all.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 10000 reads
+ samtools view -r GROUP-SRR1972919 all.bam
+ samtools fastq -t -1 all_SRR1972919_1.fq -2 all_SRR1972919_2fq -
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2000 reads

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