epiqc scripts

Scripts for data processing, analysis and visualization of EpiQC methylation data.

SLURM scripts

Scripts to be run on HPC (submitted to scheduler using SLURM). This folder includes scripts for:

• adapter trimming
• running each methylation pipeline (bwameth.slurm, Bismark.slurm, BitMapperBS.slurm, BSseeker2.slrum)
• downsampling bedGraphs generated by each methylation pipeline
• merging replicates into one bedGraph per library (e.g. combining bedGraphs from MethylSeq HG001 replicates 1 and 2)
• creating a timing comparison across all pipelines

Rmds

R Markdown files that produce figures from analysis outputs. This includes:

• Mapping.R: generate figures for mapping efficiency and CpG detection
• CpG_Coverage.R: to generate figures for genome-wide CpG coverage and genomic annotation
• CpG_Methylation.R: to generate figures for global methylation percent estimations
• AlgoComp.R: to generate figures for comparing the outputs from each methylation analysis pipeline

bin

Scripts to transform outputs in preparation for figure generation. This includes:

• downsample_bedGraph.py: normalize CpG coverage to a given mean value
• combine_methylation_outputs.py: merge signal from multiple bedGraphs (leveraged in mergeReplicates.slurm)
• combine_methylBedGraphs.py: merge signal from 5mC data in methylBedGraph format (created by e.g. Megalodon)
• bsseeker2_to_bedGraph.py: to pull CpG data frm BSseeker2 outputs and store in bedGraph format