Bioinformatics Data Analysis

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:

    
Other Messages
Messages printed to the standard error stream:
+ ACC=AF086833
+ SRR=SRR1972739
+ N=10000
+ REF=refs/AF086833.fa
+ mkdir -p refs
+ efetch -db=nuccore -format=fasta -id=AF086833
+ bwa index refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ fastq-dump -X 10000 --split-files SRR1972739
+ R1=SRR1972739_1.fastq
+ R2=SRR1972739_2.fastq
+ bwa mem refs/AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq
+ cat SRR1972739.sam
+ samtools sort
+ samtools index SRR1972739.bam
+ samtools flagstat SRR1972739.bam

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