Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • exome CNV: remove duplicate reads?

    Hi all,

    I just want to know if you remove the duplicate reads when detecting CNVs using whole exome sequencing data. It seems that for SNV calling duplicate removal is widely accepted. How about CNV detection?

    Thank you.

  • #2
    Hi,

    Yes, PCR amplification distorts the signal of expected correlation between underlying copy number and read depth. Therefore, it makes sense to try and remove the reads that are clearly duplicates and artifacts of the PCR. Of course, there may be more subtle sample-specific and target-specific artifacts (or reads not marked as duplicates, depending on the stringency of the marking), so it's still necessary to "clean up" the data to detect copy number.

    We describe in our recent paper our approach to doing this, which includes both data-driven normalization using PCA (principal component analysis) and using an HMM (hidden Markov model) to statistically genotype CNV:
    Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. American Journal of Human Genetics, 91:597-607, Oct 2012.



    And, XHMM, our downloadable software for detecting CNV from exome data can be found here:


    Best,
    Menachem

    Comment


    • #3
      Thank you very much Menachem. It is great to have published papers to support the duplicate removal. And thanks for the software. I will try it.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Non-Coding RNA Research and Technologies
        by seqadmin




        Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.

        Nobel Prize for MicroRNA Discovery
        This week,...
        10-07-2024, 08:07 AM
      • seqadmin
        Recent Developments in Metagenomics
        by seqadmin





        Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...
        09-23-2024, 06:35 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 10-02-2024, 04:51 AM
      0 responses
      103 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-01-2024, 07:10 AM
      0 responses
      111 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-30-2024, 08:33 AM
      1 response
      114 views
      0 likes
      Last Post EmiTom
      by EmiTom
       
      Started by seqadmin, 09-26-2024, 12:57 PM
      0 responses
      20 views
      0 likes
      Last Post seqadmin  
      Working...
      X