Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BWA and gaps

    In the BWA manual, I see options referring to "gap opens" and "gap extensions". What does this mean? Also, for a typical user who wants to identify SNPs, indels, etc. in a data set, is there are the default options with regard to gaps likely pretty optimal? I realize that you can always tweak stuff, but I started wondering more about messing around with gap options when I saw a paper refer to "gap-enabled BWA". This made me concerned that without messing around with these options, my BWA was not "gap-enabled", but as far as I can tell, the default options are good for dealing with gaps.

    Thanks.

    Eric

  • #2
    Originally posted by efoss View Post
    In the BWA manual, I see options referring to "gap opens" and "gap extensions". What does this mean? Also, for a typical user who wants to identify SNPs, indels, etc. in a data set, is there are the default options with regard to gaps likely pretty optimal? I realize that you can always tweak stuff, but I started wondering more about messing around with gap options when I saw a paper refer to "gap-enabled BWA". This made me concerned that without messing around with these options, my BWA was not "gap-enabled", but as far as I can tell, the default options are good for dealing with gaps.

    Thanks.

    Eric
    It is enabled by default in BWA, but gap-enabled distinguishes it from similar pieces of software which aren't gap enabled, or even gap capable, which of course isn't a selling point so much as being gap enabled.

    Comment


    • #3
      Originally posted by rskr View Post
      It is enabled by default in BWA, but gap-enabled distinguishes it from similar pieces of software which aren't gap enabled, or even gap capable, which of course isn't a selling point so much as being gap enabled.
      Thanks. That makes sense.

      And to the other part of my question: What are "gap opens" and "gap extensions"?

      Thanks.

      Eric

      Comment


      • #4
        the penalty of of a contiguous indel of length L is scored by F(L) = O + L*E, where O is the gap open penalty and E is the gap penalty. The first gap in the indel is scored (O+E), while the following gap (extensions) have score E. I would recommend buying an intro bioinformatics book like Jones and Pevzner.

        Comment


        • #5
          Originally posted by nilshomer View Post
          the penalty of of a contiguous indel of length L is scored by F(L) = O + L*E, where O is the gap open penalty and E is the gap penalty. The first gap in the indel is scored (O+E), while the following gap (extensions) have score E. I would recommend buying an intro bioinformatics book like Jones and Pevzner.
          Thanks, Nils Homer. I just put in an order for your suggestion on Amazon.

          Eric

          Comment


          • #6
            By the way, what is the difference with SW algorithm?

            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
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            9 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            50 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