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nanoporetech / medaka

Sequence correction provided by ONT Research
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How trustworthy is the quality score output of medaka smolecule using the --quality flag? #453

Closed AmstlerStephan closed 10 months ago

AmstlerStephan commented 10 months ago 
          > As of v1.6.1 medaka stitch can now has a [--qualities](https://github.com/nanoporetech/medaka/blob/master/medaka/medaka.py#L505) option to output a fastq file.

I was wondering how the quality scores from the network are interpreted now and if I could use the obtained quality scores for downstream analysis.

cjw85 commented 10 months ago

The quality scores are simply the log-transformed softmax output from the RNN. We've made little attempt to quantify how these scores match empirical residual error.