AlineMuyle

Hi, I am running Bonito with the following command line to study 5mC DNA methylation in the three contexts (CG, CHG and CHH): bonito basecaller [email protected] fast5 \ --modified-bases 5mC...

running megalodon with all context DNA methylation models

3

I am using megalodon to infer 5mC in all contexts CG, CHG and CHH. After some investigation, it seems that Megalodon version 2.5.0 + Guppy basecall server 6.2.1 do not...

Is option --n-ceil for reads only or also reference?

2

Hi, I have a reference which can contain a relatively high number of Ns (to correct for reference mapping bias at heterozygous sites). I was wondering if option --n-ceil for...

updated pipeline relying on pod5 file format?

10

Dear Dr Peng, I was wondering if you are considering updating your deepsignal-plant pipeline with the new compressed pod5 format? Including the resquiggle step. That would be extremely useful because...