DNA Methylation data analysis using Winnowmap

[msfalmeida]

Hi,

I have some genomic DNA data from ONT. As I am interested in repetitive elements I think it would be ideal to use winnowmap2 instead of minimap2 to map these reads but I would like to preserve the methylation information for downstream analysis. What is the recommended approach starting from a basecalled BAM file? Is there a way to input this into winnowmap or how can I otherwise keep the tags for methylation analysis?

Thank you.