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  • dwgsim for single ends simulation

    I want to use the dwgsim tool to do single end reads simulation, but i found
    the tools can't do generate the single end reads. such as:
    The input command is:
    dwgsim -N 10000 -r 0.001 -1 100 ~/db/genome/hg18.fa r0.fq
    The output file is:
    r0.fq.bfast.fastq
    r0.fq.bwa.read1.fastq
    r0.fq.bwa.read2.fastq
    I also checked the content of the fastq files:
    r0.fq.bwa.read1.fastq
    @chr1_203458592_203459164_0_1_0_0_3:0:0_2:0:0_0/1
    AGAGCAGAACTCTGTCTCAAAAAAAAAAAAAGAAAGAAAGAAGGTTTACAAATTTGTGTTGGGCCTCATTCAAAGCCGTCCTGGGCTGCGTGCGGCCGGT
    ### 100bp
    r0.fq.bwa.read2.fastq
    @chr1_203458592_203459164_0_1_0_0_3:0:0_2:0:0_0/2
    TCCTCTGTAATGGGAGAAAAAATGATAATCATGGCCATGAACAGAGGAGGACTGTGAAGTGTAAACTTAA
    ### default 70bp
    Is there anyone tell me why the software gives two bwa reads which don't
    like the single end reads and how I get the single end reads using the
    dwgsim ?Thanks!

  • #2
    Originally posted by kaile View Post
    I want to use the dwgsim tool to do single end reads simulation, but i found
    the tools can't do generate the single end reads. such as:
    The input command is:
    dwgsim -N 10000 -r 0.001 -1 100 ~/db/genome/hg18.fa r0.fq
    The output file is:
    r0.fq.bfast.fastq
    r0.fq.bwa.read1.fastq
    r0.fq.bwa.read2.fastq
    I also checked the content of the fastq files:
    r0.fq.bwa.read1.fastq
    @chr1_203458592_203459164_0_1_0_0_3:0:0_2:0:0_0/1
    AGAGCAGAACTCTGTCTCAAAAAAAAAAAAAGAAAGAAAGAAGGTTTACAAATTTGTGTTGGGCCTCATTCAAAGCCGTCCTGGGCTGCGTGCGGCCGGT
    ### 100bp
    r0.fq.bwa.read2.fastq
    @chr1_203458592_203459164_0_1_0_0_3:0:0_2:0:0_0/2
    TCCTCTGTAATGGGAGAAAAAATGATAATCATGGCCATGAACAGAGGAGGACTGTGAAGTGTAAACTTAA
    ### default 70bp
    Is there anyone tell me why the software gives two bwa reads which don't
    like the single end reads and how I get the single end reads using the
    dwgsim ?Thanks!
    Use "-2 0" to specify the second end should have length zero, since otherwise it uses the defaults.

    Comment


    • #3
      Originally posted by nilshomer View Post
      Use "-2 0" to specify the second end should have length zero, since otherwise it uses the defaults.
      Thanks! And I have already received your email on replying my question, you are so nice!

      Comment

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