Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Hello!

    Hi everyone,

    I'm Dean, a first year PhD student embarking on a three year Bioinformatics project. My project primarily involves processing & analysing methylation data derived using Microarray & Whole Genome Bisulfite Sequencing

    Learning Bioinformatics is no easy task, and I have joined so I can learn from the wider sequencing community. Hopefully, as I get more experienced, I will be able give advice back to members in the future!

    Fingers crossed,

    Dean

  • #2
    Hi Dean,

    I have a question for you in regard to bisulfite conversion and sequencing. My question is not so much related to dry lab portion, rather to wet lab. May I ask what kind of protocol you use? One of the problems that we encounter is that we must sequence a lot to get the desired depth of 30X, though our sample complexity is good enough to have low duplication rate. So, I am looking for an optimized procedure. Would it be possible for you to share your protocol with us?

    Thank you in advance and looking to hear from you!

    Cheers,
    Ali

    Comment


    • #3
      hello friend, i'm blake luby from tyler tx

      Comment


      • #4
        Hi Ali. Sorry for the late reply!

        Unfortunately my research will solely be focusing on the dry lab work (Bioinformatics), so I am unable to answer your question.

        It is worth noting that depending on protocol (library kit, sequencing technique), the degree and type of trimming during QC also changes. For example, it is not recommended that deduplication is performed if working with RRBS. In fact, different library prep kits require tailored trimming protocols, and there doesn't seem to one standout method just yet.

        If you do find the answer to your question, please share!

        Dean

        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, 03-27-2024, 06:37 PM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-27-2024, 06:07 PM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        53 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        69 views
        0 likes
        Last Post seqadmin  
        Working...
        X