Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Read runs and technical replicates

    So I've downloaded some example data from SRA archives at http://www.ncbi.nlm.nih.gov/sra?term=SRA011001 and had a question about technical and biological replicates (see attached picture for a snapshot of the downloads). I know that there are two biological replicates for control and treatment conditions (in this case a miR155 over-expression retrovirus) but I'm not sure about the technical replicates.

    Do read runs count as technical replicates?

    And, if so, how can I use that in my analysis pipeline (currently I'm using the Tuxedo suite (i.e. tophat > cufflinks > cuffmerge, etc.)).

    Right now I think I'm just telling the program that there are six biological replicates of each condition (i.e. 6 x miR155oe vs. 6 x control) which is probably wrong.

    Thanks, Scott
    Attached Files

  • #2
    It has been shown in many cases that Biological variation is far greater than technical variation in Illumina sequencing and typically individual runs are pooled together and treated as one sample. Ideally thats why you multiplex all your biological replicates and spread the sequencing across multiple lanes.

    Comment


    • #3
      Originally posted by chadn737 View Post
      It has been shown in many cases that Biological variation is far greater than technical variation in Illumina sequencing and typically individual runs are pooled together and treated as one sample. Ideally thats why you multiplex all your biological replicates and spread the sequencing across multiple lanes.
      Is there paper where this is shown?

      So perhaps I should merge my .sam files per biological replicate and then do the tophat/bowtie alignment?

      Thanks.

      Comment


      • #4
        Marioni, J. C., C. E. Mason, S. M. Mane, M. Stephens and Y. Gilad,
        2008 RNA-Seq: an assessment of technical reproducibility and
        comparison with gene expression arrays. Genome Res. 18: 1509–1517.

        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
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        49 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