MethylKit

MethylKit is an R package designed for analyzing bisulfite sequencing data, particularly for differential methylation analysis. It supports genome-wide methylation data and is ideal for CpG, CHH, and CHG methylation studies.

Rscript $baseDir/bin/run_methylkit.R \
        --coverage_files '${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 Methylkit_group_<compare_str>.csv .