BrdU/EdU calling in highly methylated environments

MBoemo / DNAscent

Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.

https://www.boemogroup.org/

GNU General Public License v3.0

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BrdU/EdU calling in highly methylated environments #73

Open JuandeBarba opened 3 hours ago

JuandeBarba commented 3 hours ago

Hi Michael and the team,

thanks a lot for the tool and for the recent update to 4.0.3. I am currently working with heavily 5mCG methylated DNA samples (in vitro methylation) and I was planning to analyze BrdU/EdU on the same reads. However, I was wondering if the calling of BrdU/EdU is affected by 5mC (or viceversa) and if I should take any precautions during analysis.

Thanks a lot for the time!

JuandeBarba commented 2 hours ago

Just precisions, if they are useful, I am using R10 and performing the basecalling with Dorado v7 using the High Accuracy model for 5m in CG context.