2 research outputs found
Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data
Background DNA methylation is an important epigenetic modification involved in
many biological processes. Reduced representation bisulfite sequencing (RRBS)
is a cost-effective method for studying DNA methylation at single base
resolution. Although several tools are available for RRBS data processing and
analysis, it is not clear which strategy performs the best and there has not
been much attention to the contamination issue from artificial cytosines
incorporated during the end repair step of library preparation. To address
these issues, we describe a new method, Targeted Alignment and Artificial
Cytosine Elimination for RRBS (TRACE-RRBS), which aligns bisulfite sequence
reads to MSP1 digitally digested reference and specifically removes the end
repair cytosines. We compared this approach on a simulated and a real dataset
with 7 other RRBS analysis tools and Illumina 450 K microarray platform.
Results TRACE-RRBS aligns sequence reads to a small fraction of the genome
where RRBS protocol targets on and was demonstrated as the fastest, most
sensitive and specific tool for the simulated dataset. For the real dataset,
TRACE-RRBS took about the same time as RRBSMAP, a third to a sixth of time
needed for BISMARK and NOVOALIGN. TRACE-RRBS aligned more reads uniquely than
other tools and achieved the highest correlation with 450 k microarray data.
The end repair artificial cytosine removal increased correlation between
nearby CpGs and accuracy of methylation quantification. Conclusions TRACE-RRBS
is fast and more accurate tool for RRBS data analysis. It is freely available
for academic use at http://​bioinformaticsto​ols.​mayo.​edu/​