Data Availability

All raw data is available on SRA using accession IDs SRR13050956-SRR13051274.

Please note that Oxford Nanopore long read FAST5s are available separately, using accession IDs SRR27010831-SRR27010837.

Code

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