This repository contains some scripts that I use to analyze ONT sequencing results, for which methylations were called using METEORE.
The script returns the weighted average methyaltion frequency per CpG island for a given meteore result file. Weighted, because the amount of reads that support the methylation information is used to weigh the methylation information.
This script does the first basic steps after basecalling
- merge all guppy output files into one folder
- mapping with minimap2 (https://github.com/lh3/minimap2)
- quality control with pycoQC (https://github.com/a-slide/pycoQC)
- coverage calculation with mosdepth (https://github.com/brentp/mosdepth)