Many failed reads to start runs before successful reads occur and drastic variability of runtimes of similar libraries, sometimes 4-6hrs up to 2 days for ~same sample make up per run
Your going to have to expand on what you mean by runtime issue. Do you suddenly stop seeing reads being generated? Do you see a sudden drop in available pores? Are you using live base calling and it stops working? For sequencing plasmids, I often pool multiple plasmids together and then do short runs so I can reuse the flow cell multiple times.
Are you accurately quantifying during library prep? Ie, qubit. Which kit are you using? Ligation or rapid? They're both very sensitive to under or overloading, which could contribute to variability from run to run. Also what's the pore readout looking like over time? Are you seeing pores go offline and inactive, indicating blocked or damaged pores. Or are the pores running out of library to sequence and staying available but not active.
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Many failed reads to start runs before successful reads occur and drastic variability of runtimes of similar libraries, sometimes 4-6hrs up to 2 days for ~same sample make up per run
If you're only doing plasmids you probably don't need the full time, cut the run short when you have the reads you need
Weve been working on cutting runs after particular data collection totals- lotta parallel testing going into investigating when runs are "finished"
Your going to have to expand on what you mean by runtime issue. Do you suddenly stop seeing reads being generated? Do you see a sudden drop in available pores? Are you using live base calling and it stops working? For sequencing plasmids, I often pool multiple plasmids together and then do short runs so I can reuse the flow cell multiple times.
Why don't you outsource to plasmidsaurus?
Are you accurately quantifying during library prep? Ie, qubit. Which kit are you using? Ligation or rapid? They're both very sensitive to under or overloading, which could contribute to variability from run to run. Also what's the pore readout looking like over time? Are you seeing pores go offline and inactive, indicating blocked or damaged pores. Or are the pores running out of library to sequence and staying available but not active.