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  • coverage required

    Dear all,

    I try to get an idea of the base coverage required for the different sequencing applications.
    I didn t find any review on this subject so if you know a nice paper or can complete the followings, your are more than welcome:

    - whole genome resequencing: 40x genome size (Nature 464, 587-591)
    - SNPs call: 31x genome size (Genome Res. 2010. 20: 273-280)
    - de novo genome modelling: 100x ??
    - de novo transcriptome modelling: 100x??
    - transcript expression studies: ??


    Oliviera

  • #2
    The relationship between library depth and transcript expression profiling is discussed at some length in the supplementary materials of Nature Methods. 2010 Oct;7(10):843-847 (ALEXA-Seq).

    The Trans-ABySS manuscript provides an example of de novo transcriptome assembly that might be helpful.

    Comment


    • #3
      Originally posted by oliviera View Post

      - whole genome resequencing: 40x genome size (Nature 464, 587-591)
      This amount of 'x' depend also of the size of your reads: longer reads need less coverage for the same efficiency
      Francois Sabot, PhD

      Be realistic. Demand the Impossible.
      www.wikiposon.org

      Comment

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