EdgeR

edgeR is a Bioconductor package primarily used for RNA-seq differential expression analysis but can also handle differential methylation analysis when paired with bisulfite sequencing data. This requires pre-processed methylation data, such as counts of methylated (M) and unmethylated (U) reads at each cytosine position or region of interest.

Rscript $baseDir/bin/edgeR_analysis.R \
        --coverage_files '${coverage_files}' \
        --design "${design_file}" \
        --compare "${compare_str}" \
        --output . \
        --threshold ${coverage_threshold}

options

• --coverage_files: selected from the bismark_methylation_extractor files.

• --design: selected from the Sample_sheet.csv

• --compare: selected from the Sample_sheet.csv .

Output file

• Generates EdgeR_group_<compare_str>.csv .