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  • Coverage calculation (on GA data)

    Hi,

    How to calculate coverage for Illumina Genome Analyzer sequencing data?

    Wikipedia says: It can be calculated from the length of the original genome (G), the number of reads(N), and the average read length(L) as NL / G.

    The question is how to get N?

    Kind regards
    Maria

  • #2
    Hi Maria,
    Is this de novo assembly or mapping?

    If its de novo you can calculate Number of reads for each contig as follows

    ((coverage)*(length of contig)) / (read length)

    Then you can multiply (TOTAL Number of reads) * (read length) / genome size

    If you are mapping, you should be able to pull out the number of reads that uniquely map to the genome.

    -John

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    • #3
      Originally posted by jgibbons1 View Post
      Hi Maria,
      Is this de novo assembly or mapping?

      If its de novo you can calculate Number of reads for each contig as follows

      ((coverage)*(length of contig)) / (read length)

      Then you can multiply (TOTAL Number of reads) * (read length) / genome size

      If you are mapping, you should be able to pull out the number of reads that uniquely map to the genome.

      -John
      Hi John, how do you pull out reads that map uniquely, I guess there is a flag in samformat for this? Also, what percentage of the reads that you map are duplicates and is there a way to distinguish these from PCR duplicates in RNA-seq data?
      thanks so much!
      Priyam

      Comment

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