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  • Help for bwa result

    I have short read below 200bp solexa data and used bwa for mapping,but bwa result without '@SQ lines' in the header,How can i get @SQ lines in bwa result?
    Parameter:bwa aln -l 32 -M 3 database.fa shortread.fq >aln.sai
    bwa samse database.fa aln.sai shortread.fq >aln.sam
    Anyone who can help me,Thank you very much!

  • #2
    How does your database look like? Do the reads that align show any of the contigs in your database? Do you get any error/warning while running bwa? What version are you using?
    -drd

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    • #3
      Get the latest bwa from bio-bwa.sf.net

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      • #4
        My database is fasta format and my data is fastq format ,while running bwa there is't point out any error or warning,and else my bwa version is bwa 0.5.0 (r1200)
        bwa align result doesn't show any of the contigs in database,it's special mapping.

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        • #5
          Originally posted by baby1885 View Post
          My database is fasta format and my data is fastq format ,while running bwa there is't point out any error or warning,and else my bwa version is bwa 0.5.0 (r1200)
          bwa align result doesn't show any of the contigs in database,it's special mapping.
          Yeap, that's a very old version get the latest bwa.
          Once again, I don't know where people gets this old versions.
          -drd

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          • #6
            Yeah,I have find the resourse of the problem,The versions is too old to use,and I download latest versions without this problem,Thank you again drio and lh3!
            Last edited by baby1885; 06-05-2010, 05:25 PM.

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