10x scRNAseq samples with similar reads/cell but vastly differing UMI/cell
Been trying to get my had around some discrepancies between a couple of 10x datasets. Both were sequenced to a depth of ~500k reads total and 2-3k cells yielded but then give vastly different UMI/cell as final output from CellRanger (v3). Here are further details + screenshots from CellRanger, any possible explanations appreciated!
Dataset 1 is from an in vitro cell culture experiment, yielding 3.6k cells with roughly 127k reads/cell and what seems like a very large 40k UMIs/cell:
Dataset 2 is whole tissue, yielding a lesser 2.2k cells and so a greater starting depth of 213k reads/cell. However this provides only 3k UMIs/cell – obviously much lower than in Dataset 1 despite the higher number of reads/cell:
Not sure how to account for a discrepancy this large? Mapping stats seem largely similar although some increase in rates for dataset 1. To me it could imply either a much greater amount of PCR duplication in Dataset 2 or a lack of accounting for PCR duplication in Dataset 1 for some reason… No idea why though at this stage!
Thanks for any suggestions
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