DNA Methylation


Whole Genome Bisulfite Sequencing (WGBS) and Reduced Representation Bisulfite Sequencing (RRBS) are next-generation sequencing (NGS) application that profile the DNA methylation patterns genome-wide at a single-base resolution to help understand its influence on gene expression.

General Workflow

DNA methylation utilizes bisulfite sequencing to detect methylated cytosines in genomic DNA. In this method, genomic DNA is treated with bisulfite. After treatment unmethylated Cytosines (C) will be converted into Thymidines (T), whereas methylated and hydroxymethylated Cs will stay Cs. DNA is then cloned into a library, amplified and subjected to NGS.

Data Analysis

SciDAP is a no-code bioinformatics platform that enables biologists to analyze NGS-based data without a bioinformatician. It has built-in pipelines based on open-source workflows to analyze DNA methylation. SciDAP starts from the FASTQ files provided by most DNA core facilities and commercial service providers. Starting from raw data allows SciDAP to ensure that all experiments have been processed in the same way and simplifies the deposition of data to GEO upon publication. The data can be uploaded from the end-users’ computer, downloaded directly from an FTP server of the core facility by providing a URL, or from GEO by providing SRA accession number.

Steps in the SciDAP DNA Methylation workflow


Start with FASTQ files

Using local files or public data accessions
bisulfite-seq fastq or public accession number

Read Mapping

Map reads to reference genome, and create tracks for viewing data on IGV browser
align reads to reference genome with Bismark bisulfite mapper which uses bowtie

Determine Methylation State

Infer methylation state and bin by context
infer methylation state with Bismark methylation caller

Generate Bismark Report

Summarize methylation statistics for report
run Bismark alignment report to generate a graphical HTML report page

Browse Methylation State using IGV Plugin

Generate genome-wide cytosine bedGraph for IGV
infered methylation state converted to bed for viewing in IGV

Methylation Analysis

Differential methylation analysis with RnBeads
examine differential methyltation between groups of samples

SciDAP is so easy to use and saves so much time, now biologists can produce publication-ready results in hours not months.