BS-seq is an important method for analysis of DNA methylation. It provides a snapshot of a cell's epigenomic state and reveals genome-wide cytosine methylation at single base resolution. One of the powerful tools for BS-seq data analysis is Bismark suite. Bismark can discriminate between cytosines in CpG, CHG and CHH context and allow to visualize and interpret methylation data. Output data can be mapped to genome viewer. In this tutorial, we demonstrate basic usage of Bismark in InsideDNA platform.
Cytosine methylation of DNA is an epigenetic mechanism which plays an important role in control of gene expression, silencing or genomic imprinting. Next generation sequencing allows three different methods to study DNA methylation: methylated DNA immunoprecipitation (MeDIP-Seq) or methylated DNA binding domain sequencing (MBD-Seq) and direct sequencing of sodium bisulfite-treated DNA (BS-Seq). Bismark is a suite of seven tools for efficient analysis of BS-Seq sequences. Basic pipeline includes bismark_genome_preparation tool for preparation of reference genome; bismark tool for alignments of bisulfite-treated reads to a reference genome and cytosine methylation calls; and bismark_methylation_extractor script which extracts the methylation call for every single C analysed.
In this tutorial, we will explain how to use Bismark within InsideDNA both through the UI interface and console. You can download entire dataset for this tutorial here or by clicking on Download data button at the top of the page. Read more: