Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BWA Mismatch

    Arggggggggggh! l ast chance for someone to save my life, because unless i get a definitive answer, i am going to blast my brains off on this one! How do you set a mismatch option for paired end alignment in BWA.? I was looking up the forum and was driven nuts by all the options and various parameters. I never ended up with a one mismatch alignment in the end. Can someone give me the definitive parameters for one mismatch in BWA? prettty pleaaaase? i promise lots of cookies to be couriered to anyone who helps me out on this

  • #2
    -n 1
    (waiting for the cookies)

    Comment


    • #3
      Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


      I went through this thread and tried what davetang suggested, using simulated reads. Turns out he is right. Its not just the n option which defines the mismatch

      Comment


      • #4
        That thread is 2010, with a much older version of BWA. What's wrong with -n 1, show some example?

        Comment


        • #5
          Oh k been a while since my last post. sorry i could not reply earlier as i dont have access to a decent computer mainframe. I need to book my slot to run my computations. SO anyways i tried doing what was suggested, with n-1 and l-10000 effectively to disable seeding, and I am still scratching my head here.

          Can anyone let me know how if there is a best hit criteria? Apparently I was lead to believe that the default option in BWA i.e. where we do not specify any parameters while using the aln option in sampe, is a "best hit" option which generates the "best" alignment, i.e. an alignment from all different alignments which has optimal read alignment. Looks like I need to study alignment in depth to better solidify my knowledge.

          I had generated an alignment using these default options and i found that a certain no of reads i.e. X reads were aligning. Now when i use the n-1 option which is alowing one mismatch, in theory i should have gotten Y no reads aligning, where Y>X but alas I am getting the exact oppposite.

          Thanks for all the help till now. ANd yes i think you deserve your cookies.

          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
          67 views
          0 likes
          Last Post seqadmin  
          Working...
          X