In this project, I reproduced the results from Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation (research paper here).
Briefly, with newer version of basecaller and tombo methylation caller, I validated the results from analysis of original author’s work - successfully identified known imprinting control regions (ICRs) as well as some novel differentially methylated regions.
For more detailed information, please see the original author’s work at his repo.
This repo contains scripts and notebooks used for:
- mapping reads to reference genome
- haplotyping reads (to paternal or maternal strain)
- tombo resquiggling
- call methylation with tombo and nanopolish
- plot per-read methylation patterns at known ICRs
- detect novel differentially methylated regions