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Old 02-05-2019, 05:06 PM   #1
ShyN
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Exclamation iSeq, High Q30% but Low PF%

So there's not a lot of data for iSeq since its pretty new - but if anyone has had this issue on MiSeq or in general sequencing please help!

We did an iSeq run today and the results had high Q30% (94%97%) but a VERY low PF% (19%)

What could cause this kind of variation? I've found answers for the other way around but not this.

We're considering the demultiplexing having gone wrong and we're working to correct that but if anyone else has experienced this error - what was the reason, and if it was demultiplexing how did you resolve or get a higher PF%? Is that something we can calculate as we can't get that data from the machine after our data work.
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Old 02-06-2019, 10:42 AM   #2
misterc
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Load up the run with SAV and see what the reported occupancy is. If it's below 90%, you've got too little library in there and need to increase the loading concentration. If it's 96% or higher, you've way over-loaded library and need to do the opposite.
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Old 02-06-2019, 02:54 PM   #3
ShyN
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For some reason, we can't see the reported occupancy on SAV for iSeq but we can for NovaSeq

Last edited by ShyN; 02-06-2019 at 03:03 PM. Reason: Wrong response
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