Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

    Comment


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

      Comment


      • #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.

        Comment


        • #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

          Comment


          • #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.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Yesterday, 06:37 PM
            0 responses
            8 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            8 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            49 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            66 views
            0 likes
            Last Post seqadmin  
            Working...
            X