README.md

methyl_longRead_wf

a snakemake workflow to compute methylation activity of genes with long read sequencing and associate with gene expression

how to install pipeline

$ git clone [email protected]:sahuno/methyl_longRead_wf.git
$ cd methyl_longRead_wf

option: install snakemake conda environment

Run pipeline

option: install snakemake conda environment

# conda activate snakemake #activate conda env
#MUST: create `config/samples.yaml` to match paths to per_read_modified_base.txt of each sample
#MUST: edit `config/config.yaml` to set ref genomes

$ sh run_snakefile.sh

inputs

1. samples.yaml file specifying sample name and file paths to megalodon per read modified bases file

outputs

QC

there are a number of qc available

1. calculate depth at each CpG site

$ sh samtools_depth_qc.sh '/path/to/megalodon_results_dir' '/path/to/CpG_sites_0based_mm10.bed'

notes on scripts

scripts/R: aggregate_per_read_5mC_5hmc_main.r - gather reads per site, calc mean/median methylation for 5mc methyl_activity_X_gene_expression_and_promoters_pipeline.r - associate gene expressin with promoters dseq2_analysis.r - dseq2 analysis
methylation_activity_gene_expression_and_promoters.r files_mod_bases2yaml.yaml
plot_methylation_TransposableElements.r gene_promoters_with_encode.r
plot_samtools_depth_coverage.r make_sample_yaml.r
plugNplay_any_granges.r mergeStats_ONT.r
promoter_methylation_knownGenes.r