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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.

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nanodisco score

asershova opened this issue · comments

commented

Dear Alan,

Thank you for the great tool. Could you please explain how a methylation score in the Motifs_occurrences_scores file is calculated?
Regards,
Anna

commented

Hello @asershova,

Scores found in Motifs_occurrences_scores_<base_name>.tsv correspond to maximum of the current difference averaged for a [-2, +3] window around the modified base in each motif occurrences (by default). If this help, you can find the code here. Those scores were computed in the intent to evaluate putative misassemblies in metagenomic assemblies (example in Figure 5d).

Best,

Alan