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nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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Setting up input for epigenetic modification detection #324

Open GianlucaMattei opened 2 years ago

GianlucaMattei commented 2 years ago

Hello, I would like to run 5hmC and 5mC detection.

in this case should I use the _dna_r9.4.1_450bps_modbases_5mchac.cfg or the _dna_r9.4.1_450bps_modbases_dam-dcm-cpghac.cfg to detect all the methylated Cs (not only the in the GpGs context) ?

What is the difference between the two configs and is there any description about them anywhere?

About --ref-mods-all-motifs: is "N 0" correct (to retrieve also other types of modifications) or I should just use "C 0" ? (I was looking at this https://github.com/jkbonfield/hts-specs/blob/methylation/SAMtags.tex#L477)

marcus1487 commented 2 years ago

The dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg model was an initial proof of concept model and is not recommended. The dna_r9.4.1_450bps_modbases_5mc_hac.cfg model is an improvement over this and is the best model for R9 data. Though the best results for all-context modified base detection can be achieved with kit14 and the Rerio all-context Remora model. We will continue to develop updates for kit14 models, but are unlikely to update R9 models at this time.