DNA methylation profiling from high-throughput sequencing data

In this chapter we will review the common steps in the analysis of whole genome singlebase-pair resolution methylation data including the pre-processing of the reads, the alignment and the read out of the methylation information of individual cytosines. We will specially focus on the possible error sources which need to be taken into account in order to generate high quality methylation maps. Several tools have been already developed to convert the sequencing data into knowledge about the methylation levels. We will review the most used tools discussing both technical aspects like user-friendliness and speed, but also biologically relevant questions as the quality control. For one of these tools, NGSmethPipe, we will give a step by step tutorial including installation and methylation profiling for different data types and species. We will conclude the chapter with a brief discussion of NGSmethDB, a database for the storage of single-base resolution methylation maps that can be used to further analyze the obtained methylation maps.This work was supported by the Ministry of Innovation and Science of the Spanish Government [BIO2010-20219 (M.H.), BIO2008-01353 (J.L.O.)]; ‘Juan de la Cierva’ grant (to M.H.) and Basque Country ‘Programa de formación de investigadores’ grant (to G.B.)