README

Genomics Analysis

breaks_and_joins

Functions used for making breaks and joins of the assembly

phaseFixing

Functions for correctiong out-of-phase heterozygous SNPs.

pb_SV_analysis_functions.r

Functions used for filtering and genotype calling from pbsv output.

example_genotype_calling_script.r

Exampe of how to use pb_SV_analysis_functions.r to filter and call genotypes

Methylation/DMR Analysis

dmr_pw_counts_pe.py

Does pairwise comparisons of methylation from allC files for a given set of regions and outputs to a file; results include per-sample number of methylated reads, unmethylated reads, and weighted methylation for each region

dmr_pw_ztesting_pe.py

Computes the one-sided z-test pairwise between branches to identify significant differences in methylation. Uses the result of dmr_counts_pe.py as the input

bed_gene_overlap.py

Assigns genomic feature to regions

region_haplo_filter.py

Filter regions based on read coverage and number of covered positions in the region; remaining regions were used to determine methylation pseudo-alleles

region_haplo_allele_v4.py

Determine the methylation haplotype of regions for a given sample