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  • Find out if you have amplicon reads.

    Is there really no way (program, tool) to tell if your BAM files have amplicon reads?

    How is everyone doing it? determining a priori and using different analysis pipelines? or is this done by visually judging FastQC reports?

    Any comments are welcome, I simply cannot believe we have no way to automatically tell if the reads are amplicons by library design; like, you would probably expect a really smaller number of equal start-end positions for PCR duplicates than amplicons, right? or at least less positions with duplicates in the case of PCR duplicates?

    Anyway, thanks if anyone has any input!

    cheers!

    H.

  • #2
    EstimateLibraryComplexity

    Possibly running This tool and make decisions from there?

    Comment

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