Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Sequencing depth needed

    Hi All,

    I'm interested in doing some transcriptome profiling to identify differentially expressed genes between two populations.

    how much sequencing depth do I need to do a meaningful study? In the literature I've seen reports of 100 million reads on SOLID, 40-50 million on illumina, and down to 10 million 25bp reads on illumina?

    Hoping to get some advice.

    Thanks in advance

  • #2
    I think the most intuitive way is build relationship between sequencing depth and power function or some other criteria such as FDR, and decide sequencing depth according to the "detection power" you want in term of the criterion you choose. For example, you can simulate your data via poisson model (reads count of a gene follows poisson distribution) under different sample size and use some tools such as DEGseq to identify differentially expressed genes. Then, you can calculate sensitivity and specificity under different sample sizes and choose a sample size according to the sensitivity and specificity you want.

    Comment


    • #3
      What genome?

      I don't actually know the answer, but it will probably depend on the size of the genome.

      Comment

      Latest Articles

      Collapse

      • 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
      • seqadmin
        The Impact of AI in Genomic Medicine
        by seqadmin



        Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
        02-26-2024, 02:07 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 03-14-2024, 06:13 AM
      0 responses
      33 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-08-2024, 08:03 AM
      0 responses
      72 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-07-2024, 08:13 AM
      0 responses
      80 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-06-2024, 09:51 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X