Repository for scripts used for analysing next generation sequencing data (described in order below).
Supplemental script for 100bp_dmrs.v0.1.sh for collapsing/summarising DMRs
This script uses 100bp windowed methylation data to call differences across the genome in a defined context with required coverage and a defined difference. These are performed in a pairwise manner between all samples of interest.
Uses the output from 100bp_dmrs.v0.1.sh to get mC from bed files (individual mC resolution).
First step of 100bp_dmrs.v0.1.sh that makes pairwise comparisons of windows showing a defined difference in a given context.
Script to perform SNP calling from aligned bisulfite converted reads. Use on sorted BAM file.