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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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calculate optical duplicate percentage #75

Closed Kurt-Hetrick closed 5 years ago

Kurt-Hetrick commented 5 years ago

like library size, this would be an estimate due to the uncertainty of defining the grid size for considering co-localized duplicate molecules as optical/ex amp duplicates. however, this still can be used to determine if this percentage matches expectations for overall ex amp dup rate. e.g. is the opt dup pct b/w 8-12% overall, does it correlate with percent occupancy on the flowcell. if so, then this can help determine what the pcr dup rate is vs ex amp which would help in determine if there is something wrong with library prep.

would be extremely use in the case of pcr free whole genomes (i.e. is the opt dup rate near equal to overall dup rate calculated).

Kurt-Hetrick commented 5 years ago

I believe jeremy said the expected ex amp dup rate is 5-10%

Kurt-Hetrick commented 5 years ago

done