Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • PCR duplicate removal for whole genome sequencing vs. whole exome sequencing

    Hi

    I did whole-genome sequencing and whole-exome sequencing on a whole-genome amplified (WGA’d) sample and got 2% of reads removed as duplicates by whole-genome sequencing but 80% of reads removed by whole-exome sequencing.

    I then did whole-exome sequencing on an unamplified HapMap control and WGA’d HapMap control and got 25% of reads removed from the unamplified HapMap control and 50% removed from the WGA’d HapMap control.

    I used Illumina standard PE101 whole-genome sequencing protocol for whole-genome sequencing and NimbleGen exome capture (version 2) for exome capture followed by Illumina sequencing.

    Can anyone share some thoughts on the big difference between whole-genome sequencing and whole-exome sequencing of my WGA’d sample in terms of duplicate removal? All your comments will be greatly appreciated!

  • #2
    We had the same issue at the beggining, hitting >60% dupes. We had to start with more dna and use a bit bigger fragment lengths to lower the values. We now typically get 20-30% dups.

    Lets not forget that if you have 100x coverage with 100bp reads the chances of having 2 reads with the same 5' position and/or having 2 fragments having the same sequence is pretty high. So at high coverage many duplicates aren't duplicates.

    How much coverage are you getting?

    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
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 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