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  • Maq mismatch

    Hi,

    I am currently using the match function in maq to align sequence reads to a reference genome. I want to increase the mismatch to 5 or 6 but I notice that the limit is at 3. Is there anyway around this?

    thanks

  • #2
    Originally posted by kylle345 View Post
    Hi,

    I am currently using the match function in maq to align sequence reads to a reference genome. I want to increase the mismatch to 5 or 6 but I notice that the limit is at 3. Is there anyway around this?

    thanks
    You will have to use a different aligner. Aligners like BFAST, BWA, bowtie, etc (bowtie is not for SOLiD) will allow you to up the sensitivity at the expense of speed.

    Comment


    • #3
      hi

      Hey thanks for the reply,

      I am currently using bowtie since it is one of the programs that is used by our institute. I am wondering if this is the correct line to use in order to get up to 5 mismatches. If not then how would I do this?

      bowtie -y --maxbts --best -n 5 -q

      Comment


      • #4
        Originally posted by kylle345 View Post
        Hey thanks for the reply,

        I am currently using bowtie since it is one of the programs that is used by our institute. I am wondering if this is the correct line to use in order to get up to 5 mismatches. If not then how would I do this?

        bowtie -y --maxbts --best -n 5 -q
        Looks like the "-n" option can only range from 0-3.
        Code:
          -n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2)
        PM Ben Langmead or post a new thread asking how to do this with bowtie. Alternatively, you can ask your institution to use BFAST, which allows you to a priori tune for sensitivity including indels. Admittedly I am the author for the latter.

        Comment

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