Applied Bioinformatics Course Recipes

Results generated by running the recipe.

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
+ bowtie2-build refs/AF086833.fa refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ fastq-dump -X 10000 --split-files SRR1972739
+ R1=SRR1972739_1.fastq
+ R2=SRR1972739_2.fastq
+ bowtie2 -x refs/AF086833.fa -1 SRR1972739_1.fastq -2 SRR1972739_2.fastq
+ cat SRR1972739.sam
+ samtools sort
+ samtools index SRR1972739.bam
+ samtools flagstat SRR1972739.bam

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