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  • ag2024
    Junior Member
    • Feb 2025
    • 2

    Differing duplication levels in R1 vs R2

    On a recent RNAseq run we are seeing a strange effect where duplication levels in R1 are much higher than in R2. We have never seen this before, nor has anyone we asked including the core that generated the data. Does anyone have ideas? This was a SMARTer stranded kit and Illumina sequencing (not sure which, either Hiseq or Novaseq I think). The only wrinkle is that this is RNA from blood platelets, so not complete transcriptome coverage.


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  • fchatonnet
    Member
    • Sep 2014
    • 23

    #2
    Dear ag2024, I do not have many ideas, but what is the result of fastQC on these samples?
    Are the reads properly paired? Did you try to align them?
    Good luck!

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