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Old 05-13-2016, 07:49 AM   #1
Location: Boston

Join Date: May 2016
Posts: 12
Default Oxford Metrics


I am starting a huge oxford project that will generate a huge amount of nanopore sequencing runs. I have yet to start but in my preparations I am making a log of what metrics I should record and also what constitutes a failing metric from a good metric (lowest passing metric and highest passing metric).

Lib Prep:
Initial DNA input (min = 1ug, max=?)
Qubit read after Ampure
Qubit read after Myone bead elution (min=200ng, max?)

How many accessible pores
Average read length
Amount of 2D reads
Amount of 1D reads
Sequencing time

Are there others?
What are the top and bottom limits to each metric?
Things to watch out for or pluggins to utilize while sequencing is happening?

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Old 05-16-2016, 02:02 AM   #2
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Location: Hong Kong

Join Date: Mar 2010
Posts: 497

Sorry to interject my question into your thread. I think it is somewhat relevant, so I hope you don't mind.

Based on my analysis of nanopore fast5 I downloaded from ENA, I noticed there are two types of fast5 that has their 2D flag turned off: one with template events only and one with both template and complement events.

I suppose they are all 1D reads. But what's the difference between the 1D read with both template and complement events and the true 2D reads? Is it that the latter comes from one molecule but the former comes from two different molecules?
ymc is offline   Reply With Quote

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