Home Project List Latest Recipes
Login

Bioinformatics Data Analysis

Project 0  Data 21  Recipes 26 Results
View Result
Results for How to identify large scale genomic variations: AF086833, 10000

Results generated by running the recipe.

Completed
• Runtime 1 seconds • updated 5.1 years ago by Istvan Albert
Recipe Code Rerun Recipe Edit Result Delete Result

Results generated by running the recipe.

Parameters used during the run:

  • Genome accession number:AF086833
  • The number of reads:10000
File List
Files created by the recipe run:
align.bam 466.2 KB
align.bam.bai 152 bytes
flagstat.txt 409 bytes
log.txt 906 bytes
mutations.txt 0 bytes
part1 2.0 KB
part2 15.9 KB
r1.fq 1.8 MB
r2.fq 1.8 MB
real.fa 17.9 KB
recipe.sh 2.6 KB
refs/AF086833.fa 18.8 KB
refs/AF086833.fa.amb 10 bytes
refs/AF086833.fa.ann 86 bytes
refs/AF086833.fa.bwt 18.6 KB
refs/AF086833.fa.fai 26 bytes
refs/AF086833.fa.pac 4.6 KB
refs/AF086833.fa.sa 9.3 KB
runlog.txt 513 bytes
runlog/input.json 1.9 KB
runlog/stderr.txt 545 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
+ COUNT=10000
+ BAM=align.bam
+ REF=refs/AF086833.fa
+ mkdir -p refs
+ efetch -db=nuccore -format=fasta -id=AF086833
+ bwa index refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ REAL=real.fa
+ cat refs/AF086833.fa
+ seqret --filter -sbegin 1 -send 2000
+ cat refs/AF086833.fa
+ seqret --filter -sbegin 3000
+ cat part1 part2
+ union -filter
+ R1=r1.fq
+ R2=r2.fq
+ wgsim -e 0 -r 0 -R 0 -N 10000 real.fa r1.fq r2.fq
+ bwa mem refs/AF086833.fa r1.fq r2.fq
+ samtools sort
+ samtools index align.bam
+ samtools flagstat align.bam


    





        

    






    


    

        
            

                Powered by the 
                  release 2.3.6