Scripts and commands used to call CpG and GpC methylation with Nanopolish
This directory contains shell scripts used to call CpG and GpC methylation on HG002 nanoNOMe data using Nanopolish.
- align_hg002.sh: A collection of commands used to download reference genomes, prepare genomes for Winnowmap alignment, and perform Winnowmap alignment
- merge_hg002.sh: Contains command to merge Winnowmap alignments
- filter_hg002.sh: Contains commands filtering merged alignments so only primary alignments are retained
- cpggpc_nanonome_CHM13v2.0_nanopolish_call_meth.sh and cpggpc_nanonome_CHM13v2.7_nanopolish_call_meth.sh: Contains the Nanopolish command used to call CpG and GpC methylation for each genome. These scripts were called for all FASTQ files separately using nanonome_cpggpc_call_meth.sh
- nanonome_cpggpc_call_meth.sh: Commands used to run Nanopolish CpG/GpC methylation calling scripts
- cpg_nanonome_CHM13v2.0_nanopolish_processing.sh and cpg_nanonome_CHM13v2.7_nanopolish_processing.sh: Contains all steps used to process Nanopolish methylation calls into aggregated CpG and GpC frequencies. These involve heavy use of nanopore-methylation-utilities