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

2018 ◽  
Author(s):  
Maia Malonzo ◽  
Viivi Halla-aho ◽  
Mikko Konki ◽  
Riikka J. Lund ◽  
Harri Lähdesmäki
Keyword(s):  
Dna Methylation ◽  
Data Analysis ◽  
Bisulfite Sequencing ◽  
Bisulfite Conversion ◽  
Sequencing Data ◽  
Dna Libraries ◽  
Conversion Rates ◽  
Bisulfite Sequencing Data ◽  
Low Efficiency ◽  
Sequencing Data Analysis

AbstractDNA 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.AvailabilityAn implementation of the method is available at https://github.com/tare/LuxGLM/tree/master/[email protected]

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

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Maia H. Malonzo ◽  
Viivi Halla-aho ◽  
Mikko Konki ◽  
Riikka J. Lund ◽  
Harri Lähdesmäki
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Probabilistic Method ◽  
Computation Time ◽  
Bisulfite Conversion ◽  
Sequencing Data ◽  
Whole Genome Analysis ◽  
Dna Libraries ◽  
Conversion Rates ◽  
Bisulfite Sequencing Data

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, using variational inference speeds up computation time necessary for whole genome analysis. Conclusions In this work we show that taking into account technical replicates (i.e. libraries) of BS-seq data of varying bisulfite conversion rates, with their corresponding experimental parameters, improves methylation level estimation and differential methylation detection.

scholarly journals WBSA: Web Service for Bisulfite Sequencing Data Analysis

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e86707 ◽  
Author(s):  
Fang Liang ◽  
Bixia Tang ◽  
Yanqing Wang ◽  
Jianfeng Wang ◽  
Caixia Yu ◽  
...  
Keyword(s):  
Data Analysis ◽  
Web Service ◽  
Bisulfite Sequencing ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Sequencing Data Analysis
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