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  • Exome not fully covered in WGS

    Hi,

    We are sequencing both exome and whole genome at 30x coverage. I used exome coordinate bed file to intersect it with the Whole genome bam file in order to extract the exome from the whole genome. To my surprise, I got only 8 million reads of exome from the WG whereas our exome sequencing produces around 40-45 million reads. However the coding variants from this are almost same as the exome (20-22 thousands). May I know why is it like this?
    Thanks,

  • #2
    So just to be clear, you are running target exome capture and sequencing that on an Illumina machine, and sequencing whole genome shotgun on a similar machine?

    The shotgun genome data contains things other than genes ie. repeats, non-coding DNA, intergenic sequence etc, whereas in a targeted exome sequencing procedure you only have the exome. You capture the same coding variants in both experiments, but the whole genome shotgun exome will be at a far lower coverage

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    • #3
      But we are sequencing the whole genome at 30x, so it should cover the exome also at 30x.
      Thanks,

      Comment


      • #4
        Are you doing producing the same amount of data for exome and WGS?

        Comment


        • #5
          Originally posted by tahamasoodi View Post
          But we are sequencing the whole genome at 30x, so it should cover the exome also at 30x.
          By my rough calculations, 8 Mreads that are 150 long would cover a 50 Mb exome at about 30x

          50 Mreads of 100 bp each cover a 50 Mb exome at 100x.

          How did you determine that you really have 30x coverage for each sample?

          Comment


          • #6
            I calculate this by multiplying total reads by read length divided by 3000000000 (human genome size).
            Thanks,

            Comment

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