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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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What is the relationship between qs tag and base modification? #1011

Closed 1Wencai closed 2 days ago

1Wencai commented 1 week ago

Hello， For a read, is there a relationship between Q score and the accuracy of detecting base modification? Does the larger the Q score, the higher the credibility of the base modification reported by this read? Do you have a specific value for filtering qs tag? I want to detect 6mA base modification.

wencai

malton-ont commented 1 week ago

Hi @1Wencai,

The qs tag reports the mean confidence in the canonical basecall (see here for previous discussions around this).

The confidence in each modification call is reported in the ML tag. See "1.7 Base modifications" here for details.