Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BowTie Accuracy

    I am experimenting with BowTie v 1 for various length reads (75 to 200 bp). Now, my task is to find it's throughput and accuracy. But, I can't understand how to find it's accuracy. Now, I was suggested to use an fully accurate tool and compare it to BowTie in-order to find accuracy. Can anybody help me, is there any other method (because that is really time consuming work) ? Or if I must have to compare BowTie with another tool, can anybody help me which tool I can use for above purpose. Thanks in advance.

    NB: BowTie uses only substitution for finding mismatch.

  • #2
    One way would be to generate reads randomly from the genome and see if they map to the same place. Have a look at wgsim. Keep in mind that you're unlikely to get 100% accuracy with any aligner, since parts of the genome aren't uniquely mappable (depending on the genome in question of course).

    Comment


    • #3
      Originally posted by dpryan View Post
      One way would be to generate reads randomly from the genome and see if they map to the same place. Have a look at wgsim. Keep in mind that you're unlikely to get 100% accuracy with any aligner, since parts of the genome aren't uniquely mappable (depending on the genome in question of course).
      I have checked that. Issue is BowTie matches in say 120 places on 100 read. So, I cant understand how to get accuracy for those 20 places. (I use 12 as an example)

      Comment


      • #4
        Originally posted by Arupsss View Post
        I have checked that. Issue is BowTie matches in say 120 places on 100 read. So, I cant understand how to get accuracy for those 20 places. (I use 12 as an example)
        That's not an issue with any of the tools but, rather, how you seem to want to define accuracy. Particularly when dealing with sequencing errors or reads with SNPs, there will be parts of the genome that aren't uniquely mappable. What you're seeing is likely a result of that.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Genetic Variation in Immunogenetics and Antibody Diversity
          by seqadmin



          The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
          Yesterday, 07:24 PM
        • seqadmin
          Choosing Between NGS and qPCR
          by seqadmin



          Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
          10-18-2024, 07:11 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 11-01-2024, 06:09 AM
        0 responses
        27 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-30-2024, 05:31 AM
        0 responses
        21 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-24-2024, 06:58 AM
        0 responses
        25 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-23-2024, 08:43 AM
        0 responses
        56 views
        0 likes
        Last Post seqadmin  
        Working...
        X