Jared Simpson
Jared Simpson
Hi @macieksk, That is strange! It should work on PromethION data without a problem. Can you confirm this is R9.4.1? You can test whether it is a LLR issue by...
Ok, thanks for letting me know. IIRC NA12878 has somewhat low methylation compared to normal human samples. Jared
Hi, Was this resolved? Jared
Do you have any samples that are behaving as expected, or are they all like this?
Are you using the ENCODE data from the nanopolish methylation tutorial?
Ok. That encode data is for a very small region of the genome - maybe try to get the full bisulfite run to see if this isn't an issue local...
Hm, I' dont know how well ESCs will compare to a norrmal human genome (from blood?). You want the CpG file though. I'd also suggest this one, as it is...
Hard to say, can you plot a histogram of the LLRs?
Or maybe a histogram of the methylated frequency output
@mike-molnar can you look at one of our internal PromethION runs for a normal human blood sample and see if you see the same level of methylation?