Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Enough reads in Chip-Seq?

    Dear Community,

    I am new to ChIP-seq so please be gentle.

    Analyzing ChIP-seq data - public and from my collaborators - I realized that the minimum of reads is varying very much - NCBI's minimum to submit ChIP-seq is 1 million short reads I heard and I saw published data with even less than that.

    Looking at the distribution of reads in UCSC browser (by uploading the .bam files) it looks very random over the whole genome, sometimes reads are stacking up a bit.

    Here the questions:

    A) Should you normally be able to spot peaks visually?
    The peak callers take into account fragment size as well I suppose, but usually should you be able to see distinct peaks by eye?

    B) If not - if it looks all over the genome, does that mean that there are not enough reads to detect peaks reliable?

    C) How many reads would you recommend minimum for Illumina GAIIx - read length 37 - 42nt for TFs like Myc-n or NFkB-p50?

    Thank you very much

  • #2
    A) Very much so.
    B) Either that or your ChIP did not work.
    C) Very much depends on the antibody, and the portion of the genome covered by your factor. For those two, I'd start at minimum of 20 million reads, but I'd expect a need to increase the depth.

    Comment


    • #3
      thanks,

      It is expected that those factors bind a lot in the genome

      Comment


      • #4
        Indeed - but then at least for myc I know that the antibody is pretty decent.

        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
        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