Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Minimum sequencing (and coverage) requirement for human ATAC-seq libraries?

    Hi all,

    I just got some multiplexed ATAC-seq libraries done, where I got anywhere between 50-90 million reads per sample. Greenleaf's current protocol article (http://onlinelibrary.wiley.com/doi/1...b2129s109/full) suggests that anywhere > 50 mil mapped reads is good to infer open chromatin in human samples, whereas you need > 200 mil reads to footprint transcription factors. We usually do paired end HiSeq 3000 runs.

    Can anyone who has done ATAC-seq on human genome provide some insight? What raw read numbers were you shooting for? What kind of coverage is acceptable for publication? How many HiSeq or NextSeq lanes/cells did you end up using?

    I'm trying to figure out how much more sequencing we need to do in order to get results that are publishable based on the norms (mostly for coverage) but I'm not too familiar with a lot of ATAC-seq publications yet (besides the primary Greenleaf publications), so if anyone else has an input on this, I would really appreciate it! With the above mentioned metrics, I'm currently at ~3x average coverage for the entire human genome.
    Thanks so much!

  • #2
    Hi you!

    I was wondering if you got your answer. Also I saw that you used HiSeq3000. Did you used 2x75 or 2x150bp reads? I am planning to use 2x150 and I was wondering if I could "lost" small fragments information...

    Thank you!

    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
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 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
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X