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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