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  • SOAP2 -v doesn't work

    SOAP2 -v maximum number of mismatches allowed on a read

    I have tried -v 3 -v 2 -v 4 for 50bp read, but the maximum number of mismatch in the output is always 2. there are no read wish mismatch 3 or more.



    my command:
    soap -a reads/PT0012.3_1.fastq -b reads/PT0012.3_2.fastq -D genome.fa.index -m 0 -x 500000 -u 3.unmap -o 3.paired -2 3.unpaired -v 3 -r 2 -p 2




    Usage: soap [options]
    -a <str> query a file, *.fq, *.fa
    -b <str> query b file
    -D <str> reference sequences indexing table, *.index format
    -o <str> output alignment file(txt)
    -M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]
    0: exact match only
    1: 1 mismatch match only
    2: 2 mismatch match only
    4: find the best hits
    -u <str> output unmapped reads file
    -t output reads id instead reads name, [none]
    -l <int> align the initial n bps as a seed [256] means whole length of read
    -n <int> filter low-quality reads containing >n Ns before alignment, [5]
    -r [0,1,2] how to report repeat hits, 0=none; 1=random one; 2=all, [1]
    -m <int> minimal insert size allowed, [400]
    -x <int> maximal insert size allowed, [600]
    -2 <str> output file of unpaired alignment hits
    -v <int> maximum number of mismatches allowed on a read. [5] bp
    -s <int> minimal alignment length (for soft clip) [255] bp
    -g <int> one continuous gap size allowed on a read. [0] bp
    -R for long insert size of pair end reads RF. [none](means FR pair)
    -e <int> will not allow gap exist inside n-bp edge of a read, default=5
    -p <int> number of processors to use, [1]

    -h this help

  • #2
    You have to use it with some combination of -M # . I'm not sure why but that's what I've been told.

    - Steve

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    • #3
      -M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]
      0: exact match only
      1: 1 mismatch match only
      2: 2 mismatch match only
      4: find the best hits

      what‘ that mean? If i want to find alignment with 3 mismatch, how to set the parameter M?
      Last edited by baohua100; 08-26-2009, 08:32 PM.

      Comment


      • #4
        Sorry I can't help more, a co-worker told me of that difference btw SOAP and SOAP2 so that's about all I know. I'll ask him later today to see if he's figured out more of the rules.

        It would be nice if there was a better standard for documentation of Bioinformatics apps. Seems like the only way to use some of these programs correctly is to contact the author.

        Comment


        • #5
          I would like to know
          Last edited by karthikprabu; 11-25-2009, 07:45 AM.

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          • #6
            Hello everybody,

            Does anybody knows how to deal with that problem?
            I would like to work with 4 mismatches per read and I don't know how to do...

            Comment


            • #7
              I have the same problem,have anyone figured it out? pls let me know.Thanks!

              Comment

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