This RRBS Nextflow pipeline was created to discover the genes associated with differentially methylated regions from the CpG methylation patterns using MethylDackel and Metilene.
The pipeline inputs BAM files, and outputs multiple txt and bedGraph files (according to the number of samples):
- Per base methylation metrics;
- Differentially methylated regions;
- Correlation matrix and PCA;
- Heatmap with signature differences between the controls and samples;
- Genomic distribution across the hg38 reference genome of CpGs with different methylation frequencies between samples and controls;
- Genomic distribution across the hg38 reference genome of differentially methylated regions;
- Closest RefSeq genes (version from 2024-09-11) to the differentially methylated regions;
- Venn diagram of the closest genes (only if two or more samples were used as input).