Bioinformatics Recipe Cookbook
Run Parameters
Parameters used during the run:
  • Reference Genome Accession: 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
+ REF=ref
+ GBK=ref/AF086833.gb
+ FASTA=ref/AF086833.fa
+ GFF=ref/AF086833.gff
+ BAM=SRR1972739.bam
+ VCF=SRR1972739.vcf
+ LOG=runlog.txt
+ mkdir -p ref
+ efetch -db nuccore -format gb -id AF086833
+ cat ref/AF086833.gb
+ seqret -filter -osformat2 fasta
+ cat ref/AF086833.gb
+ seqret -filter -feature -osformat2 gff
+ head -59
+ bwa index ref/AF086833.fa
+ samtools faidx ref/AF086833.fa
+ fastq-dump -X 10000 --split-files SRR1972739
+ bwa mem ref/AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq
+ samtools sort
+ samtools index SRR1972739.bam
+ samtools depth SRR1972739.bam
+ samtools depth -r AF086833:1000-1005 SRR1972739.bam
+ bedtools genomecov -ibam SRR1972739.bam
+ bedtools multicov -bams SRR1972739.bam -bed ref/AF086833.gff
+ bedtools multicov -s -bams SRR1972739.bam -bed ref/AF086833.gff

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