A high-performance pipeline for differential methylation analysis

DMAP is a comprehensive pipeline for the differential analysis of methylation from high-throughput sequencing of sodium-bisulfite converted DNA. Its main features include: flexibility in the specification of the methylated sites, ability to evaluate methylation changes across multiple conditions, and ease of configuration. DMAP is based on the MOABS pipeline [1], but replaces its MCALL module, responsible for identifying base conversions and computing methylation rates, with the new tool CSCALL [2]. CSCALL uses samtools to determine coverage and conversion rates at each site of interest, resulting in fast and reliable processing, and is able to examine conversion of cytosine in contexts other than CG, whose importance in plants and mammalian embryonic stem cells is increasingly recognized. The main CSCALL output is a BED file containing coverage and conversion rates at each analyzed site; the program also generates a report of coverage and conversion rates (by chromosome and genomewide), and reports conversion rates for "lone" cytosines, an important quality control measure. Finally, CSCALL provides a filtering function that can be applied to short reads before the mapping step, which removes reads with an excessive number of unconverted lone cytosines. DMAP output consists of an automatically-generated report including tables of differentially methylated sites between conditions, plots of methylation across chromosomes and gene regions, and quality control statistics. Usage of the pipeline is controlled by a simple configuration file listing input files for each sample and all experimental conditions.