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  • BWA: mismatch setting (Does '-n 3' allow up to three mismathces?)

    Hi everyone,

    I used BWA to map my paired end sequencing data. The length of read is 74bp. I would like to allow up to 3 mismatches in one read (no seed needed). I just set "bwa aln -n 3". Is this the correct setting for my purpose?

    When I checked the mapped sam file (tag MD:Z), I saw more mismatches than three. So I am confused about mismatch settings in BWA. Can anybody help me?

    Thanks!

  • #2
    Originally posted by wwmm933 View Post
    Hi everyone,

    I used BWA to map my paired end sequencing data. The length of read is 74bp. I would like to allow up to 3 mismatches in one read (no seed needed). I just set "bwa aln -n 3". Is this the correct setting for my purpose?

    When I checked the mapped sam file (tag MD:Z), I saw more mismatches than three. So I am confused about mismatch settings in BWA. Can anybody help me?

    Thanks!
    BWA with "-n 3" will look for mappings up to four (to guarantee all up to three). Could you give an example record with more than four differences when using "-n 3"?

    Comment


    • #3
      Originally posted by nilshomer View Post
      BWA with "-n 3" will look for mappings up to four (to guarantee all up to three). Could you give an example record with more than four differences when using "-n 3"?
      Thanks, nilshomer! I just found the problem might not be the mismatch setting. I think it is due to paired end sequencing, so I got more mismatches on one end of paired reads. Is my understanding correct?

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      • #4
        I have checked single end reads mapping. If I set '-n 3', the number of mismatches are well controlled. So the problem is that I used paired end reads.

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        • #5
          Problem solved! Thanks!
          Last edited by wwmm933; 03-15-2011, 08:52 AM.

          Comment


          • #6
            in bwa:
            XM Number of mismatches in the alignment
            MD Mismatching positions/bases

            Comment


            • #7
              Well, I seem to have the same problem.

              I ran bwa for paired-end reads, and no matter what value I put in -n option
              ( I tried -n 3, -n 4, -n 7, -n 0, ... even -n 0.05 ),

              bwa finds more mismatches than I told it to do.

              And what's worse; when I blat the mismatch-containing reads, their seldom in the accurate position!

              -------

              The above are only the facts.

              It seems to me, ("seems" to me!) that the -n option restricts the # of mismatches for only one of the paired-end reads.

              When I set -n 0, I found no paired-end reads that both contain mismatches: no pairs with both XM:i:# above 0, though one read has XM:i:0 and the other can have XM:i:# as high as 21, in the small example file I saw.

              It's very confusing.

              Isn't there any options to restrict both reads to behave the same?

              I hope somebody sees this thread.

              Have a great day!

              Comment

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