> Another problem was our flow cell was malfunctioning from the start — only 623 out of 2048 pores were working.
Is this normal for the machine? Is there a better write up somewhere where they didn’t give up immediately after one attempt?
My Nanopore flow cell had nearly every pore working from the start. So I would say that is not normal. Maybe it was stored incorrectly.
I was planning on doing a similar thing (also with saliva) once I finished moving in and had a bit more time after conferences. (But, of course, I’d have to go through and actually figure out all of the mechanics and so on.)
In my experience, most inactive pores are due to a poorly prepared sample. I don't know why, but maybe it blocks or jams the pores.
When I analyzed Oxford nano pore data a few years ago, I found it to be very sensitive to skilled sample preparation. The data quality varied so much that I could tell which of my laborant co-workers (the experienced one or the new one) had prepared the sample by analyzing the data. So I expect that the authors garage sample prep maybe wasn't great.
Coincidentally, I had a colleague who worked on building a portable sequencing lab powered by a car battery. The purpose was to be able to identify viruses by DNA from a van in rural Central Africa or wherever. Last I talked to her, the technical bottleneck was sample prep - the computational part of the van lab wasn't too hard.
No, it's not "normal," but it is fairly common. When I worked in NGS, nearly 1/4 of flow cells were duds. ONT used to have a policy where you could return the cell and get a new one if it failed its self-test.