nanoporetech
understanding modified bases threshold setting in Dorado
Issue Report
I'm using Dorado v0.7.0 for all context m6A calling but I am uncertain how to interpret the --modified-based-threshold paramater.
--modified-bases-threshold the minimum predicted methylation probability for a modified base to be emitted in an all-context model, [0, 1] [default: 0.05]
Am I correct to interpret this as Dorado will report a site to by m6A modified if the methylation probability for an individual nucleotide in a single read is 5% or higher? Why is this value set so low?
As a further question, is it possible to switch between DRACH and all context using the [email protected] model or can DRACH only be achieved using [email protected]?
Hi @DepledgeLab,
You're not quite right, no. Dorado will emit the probability that a base is modified if it passes this threshold. If it below threshold, dorado is sufficiently confident that the base is not modified that it simply presumes it to be a canonical base and lists it as being skipped in the MM tag. To put it another way, dorado has to be 95% sure a base is unmodified before it will make the decision itself rather than leaving that level of filtering to the user.
There is no DRACH model for v5, no.
Hi, Could you expand on this? I don't quite understand the explanation. Does this mean that the --modified-bases-threshold changes nothing about the base call, but only if the the probability of the call being correct is written to file? Thanks!
