Bioinformatics Recipe Cookbook
Results for Computing Read Coverages: AF086833, SRR1972739
Completed
•
Runtime 9 seconds
•
updated 5.4 years ago
by
Istvan Albert
Results generated by running the recipe.
Parameters used during the run:
- Reference Genome Accession:AF086833
- SRA Run Number:SRR1972739
File List
Files created by the recipe run:
SRR1972739-multicov-coverage.txt
12.2 KB
SRR1972739-samtools-coverage-query.txt
102 bytes
SRR1972739-samtools-coverage.txt
325.1 KB
SRR1972739.bam
1.2 MB
SRR1972739.bam.bai
168 bytes
SRR1972739_1.fastq
2.6 MB
SRR1972739_2.fastq
2.6 MB
recipe.sh
2.7 KB
ref/AF086833.fa
18.9 KB
ref/AF086833.fa.amb
10 bytes
ref/AF086833.fa.ann
94 bytes
ref/AF086833.fa.bwt
18.6 KB
ref/AF086833.fa.fai
24 bytes
ref/AF086833.fa.pac
4.6 KB
ref/AF086833.fa.sa
9.3 KB
ref/AF086833.gb
42.5 KB
ref/AF086833.gff
12.2 KB
runlog.txt
1.8 KB
runlog/input.json
985 bytes
runlog/stderr.txt
836 bytes
runlog/stdout.txt
0 bytes
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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