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

ABSTRACT:

Background

DNA methylation is commonly measured using bisulfite sequencing (BS-seq). The quality of a BS-seq library is measured by its bisulfite conversion efficiency. Libraries with low conversion rates are typically excluded from analysis resulting in reduced coverage and increased costs.

Results

We have developed a probabilistic method and software, LuxRep, that implements a general linear model and simultaneously accounts for technical replicates (libraries from the same biological sample) from different bisulfite-converted DNA libraries. Using simulations and actual DNA methylation data, we show that including technical replicates with low bisulfite conversion rates generates more accurate estimates of methylation levels and differentially methylated sites. Moreover, u

SUBMITTER: Malonzo MH 

PROVIDER: S-EPMC8760685 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature