the MinION quality scores do not follow Phred expected error rates, according to a paper that is Assessing the performance of the Oxford Nanopore Technologies MinION .Each base has a quality score, I want to know how to compute the MinION quality scores .
Your question is unclear, please provide more information.
I have updated this question,thanks for any suggestion.
Quality scores corresponding to nucleotides are calculated by the software used for basecalling. Dependent on when the data was generated this is either a Hidden Markov Model (HMM) or a Recurrent Neural Network (RNN). You can't compute those basecall quality scores yourself, and I also don't understand why you would want to.
Since you are still vague in your question concerning which paper this is from I cannot help you further with that.
My question might not be clearly stated. I know I can't compute those basecall quality scores.I just want to know the detailed algorithm for quality scores.Thanks
Then try to be complete from the beginning when you ask your question.
I don't think the exact algorithms are disclosed by ONT.
That's why I can't find the related information.Thank you very much.
So are those quality scores different than what Illumina ould have? like the Q-score?
The idea is the same: likelihood of having that nucleotide at that position. But as the chemistry and signal is fundamentally different the calculation of phred scores will be different as well. But they mean the same.
In case you were not aware, ONT has their own support forum. It might be helpful to ask there as well: https://community.nanoporetech.com/posts
According to his answer C: the content of FAST5 files that are generated from MinION he won't have access to that forum.
Good point. I didn't see the other thread (where you had essentially the same suggestion).
I assumed he was working with his own reads.