├── .gitignore ├── README.md ├── convert_bam_for_methylation.py ├── convert_bam_for_methylation_cpggpc.py ├── extract_mbed_by_qname.py ├── megalodon_mcalls_to_bedGraph.py ├── methylation_R_utils.R ├── methylbed_utils.py ├── mtsv2bedGraph.py ├── mtsv2bedGraph_upperlower.py ├── parseMethylbed.py ├── split_bed_by_haplotype.py └── test ├── convert_test.sh ├── convert_test_noreg.sh ├── haplotype_extract_test.sh └── test_gmo.sh /.gitignore: -------------------------------------------------------------------------------- 1 | __pycache__ 2 | .* 3 | !.gitignore 4 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/README.md -------------------------------------------------------------------------------- /convert_bam_for_methylation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/convert_bam_for_methylation.py -------------------------------------------------------------------------------- /convert_bam_for_methylation_cpggpc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/convert_bam_for_methylation_cpggpc.py -------------------------------------------------------------------------------- /extract_mbed_by_qname.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/extract_mbed_by_qname.py -------------------------------------------------------------------------------- /megalodon_mcalls_to_bedGraph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/megalodon_mcalls_to_bedGraph.py -------------------------------------------------------------------------------- /methylation_R_utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/methylation_R_utils.R -------------------------------------------------------------------------------- /methylbed_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/methylbed_utils.py -------------------------------------------------------------------------------- /mtsv2bedGraph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/mtsv2bedGraph.py -------------------------------------------------------------------------------- /mtsv2bedGraph_upperlower.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/mtsv2bedGraph_upperlower.py -------------------------------------------------------------------------------- /parseMethylbed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/parseMethylbed.py -------------------------------------------------------------------------------- /split_bed_by_haplotype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/split_bed_by_haplotype.py -------------------------------------------------------------------------------- /test/convert_test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/test/convert_test.sh -------------------------------------------------------------------------------- /test/convert_test_noreg.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/test/convert_test_noreg.sh -------------------------------------------------------------------------------- /test/haplotype_extract_test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/test/haplotype_extract_test.sh -------------------------------------------------------------------------------- /test/test_gmo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/timplab/nanopore-methylation-utilities/HEAD/test/test_gmo.sh --------------------------------------------------------------------------------