LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis

Abstract

DNA methylation is measured using bisulfite sequencing (BS-seq). Bisulfite conversion can have low efficiency and a DNA sample is then processed multiple times generating DNA libraries with different bisulfite conversion rates. Libraries with low conversion rates are excluded from analysis resulting in reduced coverage and increased costs. We present a method and software, LuxRep, that accounts for technical replicates from different bisulfite-converted DNA libraries. We show that including replicates with low bisulfite conversion rates generates more accurate estimates of methylation levels and differentially methylated sites.\n\nAvailabilityAn implementation of the method is available at https://github.com/tare/LuxGLM/tree/master/LuxRep\n\nContactmaia.malonzo@aalto.fi