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  • Calculating depth of coverage for overlapping paired-reads

    Hi all,
    I have a question on calculating the overall depth of coverage for exome or targeted panel sequencing samples.

    As a simple example. If I have paired-end reads that overlap each other. A particular base-pair, would have been sequenced twice, once by the forward read and once by the reverse read. When calculating depth at the base, would you consider this base as having a 1X coverage or a 2X coverage. Essentially treating each individual read of a paired-end as a separate event, or considering them as as combined single event at the base?

    Thanks

  • #2
    I think it depends on the precise definition of depth you are using:
    read depth-treat them all independently
    fragment depth-count overlaps once
    de-duplicated read depth-count overlaps once, and remove PCR duplicates, cluster duplicates, etc.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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