Batch effects from sequencing samples accross multiple flow cells.
I would like to have bulk RNA sequencing of around 50-100 samples performed on a NovaSeq 6000. I am not sure how to judge potential batch effects if the samples are distributed across multiple flowcells (e.g. 20 samples per flow cell and together with samples from other studies) vs all samples on a single "exlusive" flow cell. In general would estimate batch effects from using different flow cells as rather low. Does anyone has experience with it or even better, can recommend a paper?
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