SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing.

ABSTRACT:

Background

DNA methylation has important roles in the regulation of gene expression and cellular specification. Reduced representation bisulfite sequencing (RRBS) has prevailed in methylation studies due to its cost-effectiveness and single-base resolution. The rapid accumulation of RRBS data demands well designed analytical tools.

Findings

To streamline the data processing of DNA methylation from multiple RRBS samples, we present a flexible pipeline named SMAP, whose features include: (i) handling of single-and/or paired-end diverse bisulfite sequencing data with reduced false-positive rates in differentially methylated regions; (ii) detection of allele-specific methylation events with improved algorithms; (iii) a built-in pipeline for detection of novel single nucleotide p

SUBMITTER: Gao S 

PROVIDER: S-EPMC4488126 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature