Bioinformatics Recipe Cookbook

Run Parameters
Parameters used during the run:
  • Accession number for the reference genome: AF086833
  • SRA run number: SRR519926
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
0 + 0 mapped (0.00% : 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:
10000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 mapped (0.00% : 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
0 + 0 mapped (0.00% : N/A)
20000 + 0 paired in sequencing
10000 + 0 read1
10000 + 0 read2
0 + 0 properly paired (0.00% : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : 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:
20000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 mapped (0.00% : N/A)
20000 + 0 paired in sequencing
10000 + 0 read1
10000 + 0 read2
0 + 0 properly paired (0.00% : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : 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=SRR519926
+ REF=db/AF086833.fa
+ READ1=SRR519926_1.fastq
+ READ2=SRR519926_2.fastq
+ efetch -db=nuccore -format=fasta -id=AF086833
+ fastq-dump -X 10000 --split-files SRR519926
+ bowtie2-build db/AF086833.fa db/AF086833.fa
+ bwa index db/AF086833.fa
+ bowtie2 -x db/AF086833.fa -U SRR519926_1.fastq
+ bwa mem db/AF086833.fa SRR519926_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 SRR519926_1.fastq -2 SRR519926_2.fastq
+ bwa mem db/AF086833.fa SRR519926_1.fastq SRR519926_2.fastq
+ echo '*** BOWTIE2 PE flagstat:'
+ samtools flagstat bowtie2.PE.sam
+ echo '*** BWA PE flagstat:'
+ samtools flagstat bwa.PE.sam

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