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  • Simulated reads mapping to same region - maq simulate & dwgsim

    Hello,

    I have written a CNV Simulator, which takes fasta(eg. chr22 from hg18, repeat masked, all 'N' removed) file as input and inserts CNV at random locations.
    I then generate reads using maq simulate.
    To achieve a coverage of around 20x.
    I give,
    maq simulate -d 200 -N 2466490 -1 75 -2 75 sim_read1.out sim_read2.out chr22_sim_ref_fi.fa simupar.dat

    After generation of reads and Alignment by BFAST, to verify I wrote a perl script to bin the sam file into 5kb windows and calculate how many reads map to each window.
    I find that most(>95%) of the read are mapping to only the last window.

    I read the man page, still not very clear about few issues.
    If I specify the parameters for simulate, is it necessary to provide the .dat file?
    If yes, then what kind of fastq file should I train simutrain on?
    Also the man page mentions that there is a .dat file available for download, but I am not able to find it.
    I have also tried with dwgsim now, the same problem occurs, all reads mapping to the last window.

    Can anyone point out what I am doing wrong.

    Thanking you,
    Prakhar Gaur

  • #2
    Tried with chr18.fa from hg18.
    I am getting the same results, almost all reads mapping to the same region.

    $dwgsim -d 200 -1 75 -2 75 chr18.fa out.bwa.read1.fq out.bwa.read2.fq out.bfast.fq
    then used Bfast.

    Comment


    • #3
      There is No issue with maq simulate or dwgsim.
      It was my mistake which caused the problem.
      The Perl pipeline was faulty.

      Sorry for any inconvenience caused.
      --
      Prakhar Gaur

      Comment

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