This repo includes code analyzing the following HG002 data:
- CpG methylation from PacBio HiFi reads using Primrose: wgbs_pacbio_processing
- CpG and GpC methylation calls from ONT reads from nanoNOMe experiments called with Nanopolish: nanopolish_methylation_scripts
- CpG methylation calls from ultra-long ONT reads called with Remora and Guppy 6.1.2: remora_methylation_processing
- CpG methylation calls from WGBS and EM-seq short read datasets: wgbs_pacbio_processing
Comparison of the methylation identification technologies as well as the code used to produce figures can can be found in the r_analysis directory.
The code for production of summary methylation files (bigWigs and beds) can be found in the r_analysis directory.
Steps on how Nanopolish downloaded and installed are found here: 221019_nanopolish_nanonome_setup.pdf
Information on sequencing data resources can be found here: hg002_chrY_methylation_resources.csv