Bioinformatics Data Analysis Pipeline- Methylation

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states.
Reference: PMID: 21493656
Contact: Qin Ma
TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.
Contact: Qin Ma
DSS

An R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq)
Reference: PMID: 23001152
Contact: Qin Ma
MethylKit

R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.
Reference: PMID: 23034086
Contact: Qin Ma