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troubleshooting a PromethION run - got low pore occupancy and I suspect we overloaded it. Aimed for 10 fmol but possibly added more.

Any tips for confirming or other ideas?

#nanopore @nanopore

plot of a Oxford Nanopore PromethION run showing relatively low pore occupancy over the course of the run
#nanopore @nanopore
in reply to Frank Aylward

Martin Smith
mastodon - Link to source
Martin Smith
• •
might be ligation/tagmentation efficacy. What are you sequencing and how do you calculate molarity?
in reply to Martin Smith

Frank Aylward
mastodon - Link to source
Frank Aylward
• •
@Martinalexsmith yeah I spoke to the nanopore folks and they suggested it was a ligation efficiency issue. It's euk genomic DNA and super long fragments can have low efficiency, apparently.
@Martin Smith
in reply to Frank Aylward

Martin Smith
mastodon - Link to source
Martin Smith
• •
the pore drop-off is fast as well, things are getting clogged up. If you have enough input material, you should wash and reload a few times (every 6-12h)
This entry was edited (2 years ago)

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