Bioinformatics Recipe Cookbook

Run Parameters
Parameters used during the run:
  • Accession number for the reference genome: AF086833
  • SRA run number: SRR1972739
Output Messages
Messages printed to the standard output stream:
*** BOWTIE2 SE flagstat:
10000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
6372 + 0 mapped (63.72% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
*** BWA SE flagstat:
10351 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
351 + 0 supplementary
0 + 0 duplicates
7571 + 0 mapped (73.14% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
*** BOWTIE2 PE flagstat:
20000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
12537 + 0 mapped (62.69% : N/A)
20000 + 0 paired in sequencing
10000 + 0 read1
10000 + 0 read2
9828 + 0 properly paired (49.14% : N/A)
11482 + 0 with itself and mate mapped
1055 + 0 singletons (5.27% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
*** BWA PE flagstat:
20740 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
740 + 0 supplementary
0 + 0 duplicates
15279 + 0 mapped (73.67% : N/A)
20000 + 0 paired in sequencing
10000 + 0 read1
10000 + 0 read2
14480 + 0 properly paired (72.40% : N/A)
14528 + 0 with itself and mate mapped
11 + 0 singletons (0.05% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
Other Messages
Messages printed to the standard error stream:
+ mkdir -p db
+ ACC=AF086833
+ SRR=SRR1972739
+ REF=db/AF086833.fa
+ READ1=SRR1972739_1.fastq
+ READ2=SRR1972739_2.fastq
+ efetch -db=nuccore -format=fasta -id=AF086833
+ fastq-dump -X 10000 --split-files SRR1972739
+ bowtie2-build db/AF086833.fa db/AF086833.fa
+ bwa index db/AF086833.fa
+ bowtie2 -x db/AF086833.fa -U SRR1972739_1.fastq
+ bwa mem db/AF086833.fa SRR1972739_1.fastq
+ echo '*** BOWTIE2 SE flagstat:'
+ samtools flagstat bowtie2.SE.sam
+ echo '*** BWA SE flagstat:'
+ samtools flagstat bwa.SE.sam
+ bowtie2 -x db/AF086833.fa -1 SRR1972739_1.fastq -2 SRR1972739_2.fastq
+ bwa mem db/AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq
+ echo '*** BOWTIE2 PE flagstat:'
+ samtools flagstat bowtie2.PE.sam
+ echo '*** BWA PE flagstat:'
+ samtools flagstat bwa.PE.sam

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