Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • methylation analysis - bisulfite sequencing with SOLiD?

    I was reading this article which compares the three sequencing platforms:
    http://genomics.ucr.edu/about/report...1207_Table.pdf

    The table there shows that SOLiD won't work with "methylation (bisulfite)". Does any one know WHY??

  • #2
    This is old information. The SOLiD-1 software QC module didn't like the T bias in the bisulphite sequencing reads and called these erroneous clusters. This was fixed in SOLiD-2 and now ABI are developing a very crafty method of bisulphite sequencing incorporating a non-bisulphite treated DNA "address" within the same fragment and read in a paired end strategy. Don't ask me details. The ABI guys were intentionally vague as its still in development.

    Comment


    • #3
      you can get an update on this mate pair strat if you ask.
      this method seems to be the most clever/difficult, but it would bypass the issues with refseq that all the platforms have.

      Comment


      • #4
        AB has publicly spoken about two ways of doing methylation on SOLiD. One is hemi-methylation, and I am not aware of any protocols or details other than AB's internal work they discussed on that topic. The other utilizes an Invitrogen kit for bi-sulfite conversion (the merger makes that convenient...).

        There is nothing about SOLiD that makes it incapable of methylation, AB just hasn't released a supported kit, and I am not aware of a customer who has published their data yet. There is nothing related to the platform that will limit methylation, and it will work fine but lacks AB kit chemistry and published protocols right now.

        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
        12 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
        52 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X